ThunderMax PN-309-366 User Manual

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309-466 Installation / Setup Guide V2013.09.16

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1

Part # 309-366 / 309-466 for V-Rod®
Models

Thank you for purchasing a ThunderMax ECM!

Please read through the following instructions before
beginning the installation procedure. Following these
instructions will ensure that the ECM is installed and
setup properly for optimal results. If you have any
problems or questions, please refer to the SmartLink
Tuning .pdf Manual, included on the CD (Help Menu)
with this package.

Step 1 Insert the SmartLink

CD into your computer.
SmartLink will automatically
open the InstallShield
Wizard when the computer
finds the CD-Rom. Follow
the instructions and install
the software on your
computer. If you do not have a serial port on your
computer for the communication cable, you will need to
use a USB to Serial converter (an inexpensive converter
is available from Zipper’s, #372-000). Install the included
driver disc at this time; follow the instructions given by
the manufacturer of the converter for installation.

Step 2 Install the ThunderMax and AutoTune modules.

(See dielectric grease tip for ECU on bottom of page 7)
Due to the mounting location and space constraints on
the V-Rod® for the ECM, your ThunderMax system is
supplied with a separate AutoTune module. The
ThunderMax ECM mounts in the same location as the
factory ECM; the AutoTune module mounts separately.

2002-2005 MODELS

Step 2a

Remove the
seat, air box
cover and
front frame
side covers
(2) to expose
the airbox
and battery
area.
Remove the
airbox lid with
snorkel.

Installation / Setup

Please Note: This product is Legal in

only for racing vehicles which may never be

upon a highway.

product for his or her use. Installation and use on a pollution-

controlled vehicle constitutes tampering under the U.S. EPA

guidelines and can lead to substantial fines. Review your

application and check your local laws before installing.

The user shall determine suitability of the

Guide

Locate fuse box just
forward of the seat and
remove fuse labeled

POW

“ECM
fuse, right side).

Unplug and remove the
factory ECM from the
motorcycle (located just
behind the steering
stem).

Due to the tight restrictions of the location of the ECM on
2002-2005

Option 1 - The

communication

cable can be
installed into the
communication port
of the ThunderMax
ECM

attached

ECM and stored on

the motorcycle

(how you

route/store

cable is up to you, you can run it through the frame and
along the airbox housing and store it under the seat or
roll it up and store it under one of the side covers), or
Option 2 –(PREFERRED not required) Install
ThunderMax Pigtail Communication Port Harness
( i nc l u d ed) and wire it to the ECM harness plug on
the motorcycle for an alternate port location.

Once option 1 or 2 is performed, install the ThunderMax

ECM to the motorcycle in the stock location. Plug the

main harness into the ECM and reinstall the ECM fuse.

ER” (center

model bikes:

and

remain

to

the

the

California

used

th

e

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2

Either

of

these

options

will

allow

Step 2b Remove

2006-UP MODELS

the front and rear
seat, air box cover
and front frame
side covers (2) to
expose the airbox
and battery area.
Remove the airbox
lid with snorkel.

Step 2c Trial fit the

ThunderMax to the
plastic ECM caddy.
Note that some parts
of the caddy will need
to be modified for
proper fit. This is
easily accomplished
with a saw blade.

Cut the caddy in three
places as shown and
remove the ‘T’ shaped
section. Trial fit the
ThunderMax ECM into
the modified caddy; re­trim as necessary. Re­install the caddy with
the ThunderMax ECM
in place.

Locate and remove
the ECM fuse.
Unplug the ECM and
remove the ECM with
the plastic ECM
caddy (unsnap the
caddy from the
fender). Separate the
ECM from the caddy.

Remove the
“loop” from the
left side of the
caddy with a
hacksaw blade or
similar cutting
tool.

Plug the ECM main

harness into

the
ThunderMax and
reinstall

the ECM
fuse. At this point,
you have two options
for linking to

the
ThunderMax with the
supplied
communication

Option 1

cable:

- The
communication cable can be installed into the
communication

port of the ThunderMax ECM and remain
attached to the ECM and kept stored on the motorcycle
under the seat, or
Option 2 – Install t h e ThunderMax Pigtail
Communication Port Harness (included) and wire it to the

ECM harness plug on the motorcycle for an alternate port
location.

quick communication
with the ThunderMax
without removing the
passenger seat to
plug in the cable.
Reinstall the
passenger seat.

ALL

MODELS

Step 2c Install the supplied wide band oxygen sensors

into the exhaust pipes. If your exhaust system is not
equipped with oxygen sensor bungs, they must be
added to the exhaust pipes. The supplied wide band
sensors are longer than the factory sensors. Installation
of the wide band sensors into factory headpipes
equipped with bungs should present no clearance
problems, however, some aftermarket pipes may require
exhaust pipe modification or sensor bung relocation for
interference-free installation. The sen
freely without contacting surrounding components. If

this is not possible, do not attempt to bend or
modify the sensor in any way as it is a sensitive
electronic component and will be damaged if you do.

Modify the pipe if required for clearance.
are available for exhausts systems not equipped with
bungs or if current bungs present clearance issues.
Bungs should be located no more than 3-4” from the

head/pipe connection (for ideal location, refer to the
factory location on 2008-up models).
available from Zipper’s (#272-200, straight; #272-202,
angled). After installation, route the sensor harnesses
through to the left side of the bike as shown.

sors must mount

W

eld-in bungs

W

eld-in bungs are

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Locate the gray 4-pin data link
port connector near the frame
neck behind the louvered side
panels (left side on ’02-’05, right
side on ’06-up models) and
remove the rubber plug from it.

Install the AutoTune
module flat side up, wires
toward rear. Slip loose wire
ties over front airbox cover
mounting tabs, pull wire ties
tight so that the AutoTune
module is mounted to the
bottom of the bracket as
shown.

Plug the oxygen sensor
harness into the AutoTune
harness plug marked
“FRONT”. Avoid routing
harnesses where engine
movement or moving parts
can contact and damage
the harnesses or connector
plugs.

Loosely loop a wire tie
through each slot in the
supplied AutoTune
module.

Route the oxygen sensor
harness from the front pipe
along the left frame
downtube, across to the
right side of the frame in
front of the cylinder head
cover, away from the
engine and along the frame
when possible.

Plug the 4-pin AutoTune
connector into the gray data
port connector. It is
through the data port that
data from the AutoTune
module is transferred to the
ThunderMax.

Route the rear oxygen
sensor harness between
the engine and fuel tank
under the seat . The
AutoTune harness for the
rear cylinder sensor is
shorter and can be easily
identified by black tracers
on all of its wires; both
plugs are clearly marked for
front/rear use.

poorly! Tie the harnesses

Route the harness along
the upper left frame rail
and

plug

the oxygen
sensor harness into the
AutoTune harness
marked

“REAR”.

It is
very important to install
these correctly

or the
engine will perform
to the frame or existing

plug

component harnesses, taking care to avoid contact with
any vibrating component that may chaff the sheathing or
wires. Some disassembly of bike components may be
required for best harness routing.

Some riders prefer to remove the airbox lid altogether for

increased airflow to the intake. If you chose to leave it

on, the “snout” must be removed due to the AutoTune

W

module mounting.

cutting tool, cut the airbox snout off the airbox lid.

Reinstall the airbox and frame louvered covers.

ith a hacksaw blade or similar

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Step 3 Load a Base Map to your SmartLink software.
Selecting a base map for your ThunderMax is easy
thanks to the filtering system in the SmartLink software.
Open SmartLink on your computer. The first time the
program opens, you are asked which platform you’ll be
working in, Big Twin or V-Rod. If the program was
opened in standard Zipper’s (Big Twin) configuration,
change the configuration by selecting from the toolbar

[Configure] [Product Configuration] [TMax V-Rod].
From the toolbar choose [EFI Maps] [EFI Map List

ings

/ Definitions]. You should first update the Map

Definitions file to ensure you have the latest available
maps. Close the [Base Map Definitions] window, then
click the [Check Internet For Updates] button (requires
internet connection; follow prompts). After updating,
select [Select BaseMap].

Available base maps will be shown (if the [Show all
Maps] button at the lower left of the screen is
highlighted, click it to clear filtered maps so all maps will be
shown).

Filter the maps to locate a base map that best matches
your application by placing your curser first over any
‘Engine Type’ that matches your engine and right-click it.
All maps that do not match your selection will be filtered
from the screen.

Second, place your curser over the ‘Throttle’ column
and right click your match.

Third, right-click the ‘Exhaust’ type that closest matches

your application.

Fourth, right click the ‘Muffler’ column if further definition

of the exhaust system is required (depends on exhaust

application). Keep right-clicking the application columns
until you have located the best map match (in the case
of identical maps, choose the latest date). Highlight the
map you’ve chosen (left-click; blue bar indicates
selected map) and click [Close] button. This brings you
to the ‘Base Map Name Encoding’ page, from which you
can review the map parameters. Click the [Load
BaseMap] button to load the

From this page you can load the base map into the
software by clicking the [Load Base Map] button.
[Close] this page to view the open map page.

map into the software.

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V-ROD®

2002-2003

26250

V-ROD®

2004-up

28000

Step 4 From the ‘Tuning Maps’ Tree, click the + sign
next to [Module Configuration], then double-click
‘Basic Settings’. The basic settings page opens.
Check to see if the [Speedo Cal] calibration setting
matches your year and model; if not, click the button,
enter the correct value as shown, then click [Close].

Speedometer

Calibration

Settings

Step 5 Now you are ready to ‘Link’

‘W

and
Attach the communication cable
from your computer to the
ThunderMax module, making
certain that the cable is routed away
from any part of the motorcycle that
generates heat.

Special Note for International Model Bikes with
Active Exhaust Enabled: If your bike is equipped with

a working Active Exhaust Valve, you must unplug the
active exhaust harness before linking to the module, as

the AEV circuitry conflicts with the communication
stream. You can re-connect the harness after unlinking.
If the stock exhaust has been changed, disregard this
step. ThunderMax does not support active exhaust

Step 6 To link to the module, turn the key switch to the

“Ignition” position, making certain the “RUN / OFF”
rocker switch (Kill Switch) on the handlebar controls is in
the “RUN” position. Select the “Link” Button in the
SmartLink software. The button turns green to indicate a
successful link. Answer [No] to the “Do you wish to
READ the module map now” question at this time.

rite’ the map to the ECM.

From the toolbar, click [File] [Write Module Maps and

Settings], answer OK to the message that informs you
that you are about to overwrite the current map in the

module; the transfer bar appears during the map load.

Step 7 Verify Module Settings. Before performing this

W

step, clear any active Diagnostic Code readings.

hile

linked, from the Tuning Tree select [Module

Configuration] [Diagnostic

Codes].

When the Diagnostic Codes window appears, select

[Clear Diagnostic Codes]. After completing this step,
select Basic Settings from the Module Configuration
menu and verify that the speedometer calibration is
correct. After verifying these settings, click [Write Basic
Settings]. If the installation is to be operated in closed
loop mode (with AutoTune module), select

[Configuration] from the toolbar menu and click
[Closed Loop Configuration]. Verify that the [Closed
Loop Processing] and [AutoTune] boxes are che

cked

√ on the left (module) side of the window.

IMPORTANT STEP BEFORE STARTING

Next, ‘Initialize’ the ThunderMax ECM. Initializing

synchronizes ‘home’ positions for the TPS and IAC, and

is a required step any time battery power has been

interrupted or established to the ThunderMax ECM.

With the handlebar switch in the ‘ON’ position, cycle
the key switch on and off 3 times, leaving the
ignition on for 30 seconds, then off for 30 seconds,
each cycle. DO NOT start the engine or move the

throttle during this process. After 3 on/off cycles, make
certain that the motorcycle is in neutral and start the bike

2 times, letting it settle at idle for 10 seconds; the idle
should be smooth and steady. Some engines may
require several on/off engine starts to initialize properly.

This initialization process must be performed any

time battery power is interrupted to the module (after
battery

servicing/winterization,

etc). After initialization,

shut off the engine, but stay linked for step 8.

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Step 8 Before restarting the engine, from toolbar click

[Monitoring] [Show Gauges]. The “Engine Speed”,

“Engine Head Temp”, “IAC Position”, “AFR Front”, AFR
Rear” and “AFR Target” gauges are automatically
formatted and are shown on the screen. Additional
gauges can be created if desired (see SmartLink Tuning
Manual under Help menu), but the above gauges are
most helpful during initial set up. You may select any
gauges that you deem important; if too many are chosen
your screen may appear cluttered.

Step 9 Select the “Monitor” button to active the gauges.

It is located beside the “Link” button and will turn green
when the monitor gauge functions are live. The gauges
will be displayed if they were not already on the screen.

Step 10 Now select the IAC Stops vs. Engine

Temperature page from “IAC Curves” menu within the
tuning tree. Strike the

spacebar to show the actual values of the tuning block
(use left/right arrow keys to move the block marker).
Make certain that the motorcycle is in neutral and the
engine is cold, and then start the engine. Once the
engine idle is stable after 15- 20 seconds, select the
“IAC-Auto” button (Idle Air Control Auto Adjustment).
Allow the “IAC-Auto” function to run at idle until the
engine head temperature reaches 205 degrees. After
reaching temperature of 205 degrees, the “IAC-Auto”

function automatically shu

ts off. You can terminate this
function at any time, and re-run it at a later time if you
wish.

Step 11 Unlink the SmartLink software from the ECM,

turn off the ignition switch and remove the

communication cable from the ThunderMax ECM. Use
the ‘Save As’ command to create a folder and save the
map to your hard drive. The motorcycle is now ready to
be ridden. Several riding sessions that allow the engine

to reach normal operating temperature should be
completed. During this process, the IAC virtual stops will
automatically be adjusted to the IAC target values set
within the map’s basic settings. This feature
automatically ad justs how the engine comes back to the
specified idle speed. If the IAC stops are set too low, the
engine will dip below the specified idle speed during
certain transient conditions. If the IAC stops are above
the IAC position, the engine will idle above the idle rpm
specified in the i

dle speed vs. engine temperature page.
If it determined that these automatic adjustments have
not resulted in satisfactory operation of the engine,
consult the SmartLink Manual (available under the Help
section of the toolbar), Section 3 (Tuning the
ThunderMax ECM) for further adjustment procedures.

CLOSED LOOP PROCESSING

When equipped with AutoTune, your SmartLink software
will allow you to set Air/Fuel tuning parameters for your
ThunderMax and its installed base map. To set the
AutoTune Limits, go to the toolbar and click [Configure]
[Close Loop MODULE Settings].

The Closed Loop Configuration dialog page opens; the
right side shows the default MAP settings stored in the
MAP file (settings are applied to the installed base map
during the ‘Closed Loop Format’ conversion performed
by SmartLink), while the left side shows what the module
is currently set to (unadjusted, these settings will mirror

MAP’s settings).

The un-highlighted left ‘MODULE’ side of the page

allows editing of those settings within the MODULE for

tuning purposes, while unaffecting the MAP settings. To

edit module settings, click the [Link/Read (Module)]

button (left side highlights/active). You can now edit

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these settings within the live module should you want to change any of the settings from the MAP default
settings.

Closed Loop Processing (Module) – Check [ON] to enable closed loop AutoTune processing. During closed loop
processing, the ThunderMax module processes feedback from the oxygen sensors to adjust the fuel volume at all
points by creating learned “offset” points from the installed ‘base map’ fuel points. The ‘static’ base map is
dynamically used by the ThunderMax module and the AutoTune’s active (closed loop) feedback system. This
system optimizes the fuel points to fit the target air/fuel ratio through ‘learned offset points’. These ‘learned

offset points’ are stored within the ThunderMax and are used i

n conjunction with the base map. The ‘base map’ fuel

points are not being adjusted by either the AutoTune or ThunderMax modules.

If AutoTune Closed Loop Processing is un-checked, fuel points will be adjusted to the last learned offset points, or if no
learning has occurred, to the original base map points. Stored offset points remain within the module; in the event that
power is interrupted for any reason, the learned offset points remain until re-learned or cleared under the [Map

Editing] toolbar menu.

Air Fuel Ratio Override (Module) – A single Target AFR setting can be applied using this command.

Clicking this box and changing this number overrides ALL ‘Air/Fuel Ratio vs. TPS’ pages at all RPM’s. To
target specific Air/Fuel Ratio RPM ranges and throttle positions, leave this box unchecked and edit the
individual ‘Air/Fuel-TPS @ RPM’ map pages located under the [Tuning Maps] tree. Individual Air/Fuel targets
are pre-set within the base map to provide a good balance between power and

econom

y. Individual cell throttle
position/rpm AFR targets can be viewed and adjusted on these pages. Use the left/right arrow keys to navigate the
individual blocks (strike the spacebar to view the values);

use the up/down arrow keys to adjust the values. Click
the [Monitor] button when linked live and a vertical bar will show the actual throttle position. See the SmartLink
manual for further tuning instructions.

Idle Air Control Override (Module) - Check [OFF]. This setting should not be checked on except for diagnosing a
particular type of supported problem or during tuning on a load cell dyno. Changing this setting will lead to starting
and idling problems.

Maximum CLP Offset (Module) – [Session (Module)] button sets the AFR maximum learning correction from the
base map’s fuel setting per session by percentage (range is 0-10%). A ‘session’ is defined as the period of time from
engine on to engine off (per cycle). [Maximum (Module)] button sets the total AFR maximum learning
correction from the base map’s fuel setting by percentage (regardless of number of sessions; range is 10-25%).
Unless your application is a considerable mismatch to the installed base map, the default settings of 5 and 20
percent are sufficient for most AFR corrections.

You should always pick the best possible map match during the selection of your base map. The theory behind
this is to reduce the range and time the closed loop system needs to learn offsets (corrections) for the target AFR. If
your map selection is a poor match to the application, the amount of learning needed will be significant. Review the
parameters of your base map vs. available base maps under ‘Base Maps Listing ’ to ensure you have the best
map match and the latest version of the map.

TIPS AND GENERAL INFORMATION

A packet of dielectric grease is included with your ThunderMax.
dielectric grease to the inside lip of the ThunderMax ECM (Photo 1) and across the clear case on the 36 pin ECM
connector (Photo 2). Spread the grease across all of the female terminal openings, making sure the grease penetrates

openings. This grease will greatly improve vital

conductivity

between the ThunderMax and the 36 pin connector.

W

hen installing the ECM, apply the provided

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•

Several support features are located under the

[Help] menu; some require an internet
connection.

•

A comprehensive Tuning Manual in PDF

format is included on the CD for viewing and
printing from your desktop.

•

When the SmartLink program is opened, it

will automatically retrieve and open the last map
that was open.

•

Any time you link to your motorcycle: Read

the map that is installed in the ThunderMax
ECM by selecting [File] then [Read Module
Maps and Settings] on the SmartLink toolbar.
This will synchronize the map file loaded into the
ThunderMax ECM with the SmartLink software.

•

2003 FLT/FLHT models: H-D® used 2 different

speedometer calibrations during the extended
2003 model production. Which calibration you
may need is easily identified by checking the
part number on the back of your factory ECM.
Calibration 20480 is used if the part number
ends in -03, while 4352 is used if the ECM p/n
ends in -02. If your turn signals don’t cancel on
a 2003 model, try the alternate setting.

•

2007-up Big Twin models: There are two

settings in the [Module Configuration] [Basic
Settings] page that should to be set to the

following to enable the 6
function:

Final drive ratio [87; 84 for 06-07 Dyna®]

Gear 6 Min TPS

•

Sportster® models: The [Main Relay Loc]

must be set to “1” under the [Basic Settings]
[Module Configuration] page, or the engine will

not start.

•

Accel Fuel is be used to tune throttle

(go to [Module

•

AFR Correction vs. Engine Temperature page

Configuration]

is used to adjust cold start AFR’s. It is active yet
should be used with extreme caution. Any
changes made to this page affects all maps, at
every throttle position, every 256 RPM’s! See
SmartLink Tuning Manual for procedures.

•

AFR vs. Engine Temperature is active yet at

this time you should be discouraged from
making any changes to this page.

th

gear indicator light to

[40].

response

[Basic Settings]).

•

Air/Fuel-TPS @ RPM These pages reflect

desired targets of AFR to throttle position at
every 256 RPM. Example: if you desire a leaner
mixture for added fuel

econom

y then you can
easily make multi-tiered AFR targets at specific
throttle positions and RPM’s that will be learned
during closed loop processing.

•

During warm-up, the AFR on both cylinders will

be richer than the target AFR at normal
operating temperatures; this is a normal part of
the warm-up map. AutoTune and its targets are

inactive below 200 degrees.

•

Target air/fuel ratios can be viewed on the

Air/Fuel-TPS @ RPM pages. W hen these
pages are open, you can view the target AFR by
clicking on a dot and tapping the space bar to
view the target at a specific throttle position for
that RPM. Use arrow keys to raise/lower targets.

•

Writing new or modified maps to the module

requires the system to be re-initialized (Step 7),
and any existing learned fuel and IAC
adjustments to be cleared (Map Editing, clear).
Linking and editing an existing map within the

module does not require above steps.

•

System Updates are available through

SmartLink with an internet connection.
Software, Firmware and Map updates can be
downloaded; check

•

In-Tank Fuel Filters should be inspected as a

frequently

for updates.

part of routine maintenance. The filter is small
and one bad load of fuel can clog it. The factory
recommended

•

Save your edited maps to your hard drive

service interval is 25K miles.

using the [Save As] command. Document the
changes in [Map Notes] located under [EFI
Maps on the toolbar. These notes are stored
with the saved map; remember to edit them
when making changes for future reference.

•

Oxygen Sensor Care: Items that can damage

or shorten the life of your sensors:

Leaded fuel – Race fuel
Oil deposits from oil

consumption

problems
Excessive moisture exposure
Excessive (extreme) heat

There is no warranty on sensors. Replacement
P/N is 309-355.