LockedHonda Rubicon Shift Problems

Grass Hog
2008/04/08 20:45:14
Well I've spent the last  couple weeks  reading the previous posts on this subject and  following the manual  flow chart for troubleshooting.  This is what I've got.  It's an '01 Rubicon, when you turn the key on the "--", D1, D2 and ESP all flash, not a code, they just keep flashing the entire time the key is on. The rubi won't shift and sputters when in reverse. I did a code retrieval and got "Code 6" so I cleaned all the connectors and put dielectric grease in them. I put on a new angle sensor and pre-loaded it and tried the initialization procedure, but it doesn't seem to be working right I don't hear the control motor turn and the lights mentioned before just keep flashing. I pulled the control motor and I can freely spin the gear inside the tranny with my finger, I tested the control motor and it is good. I checked the angle sensor wiring for continuity to the ECM and it showed nothing on all 3 wires. I temporarilly re-wired the angle sensor to the ECM. Now I no longer get "Code 6" now I get "Code 11". I checked for continuity like the flow chart said and it shows an open in the wire, I'm having trouble believing that all these wires are open, counting this one and the 3 on the angle sensor that makes 4 total and that seems a little odd. Could it be an ECM problem? I really wish I knew someone in the area with a Rubi so I could do an ECM swap without having to buy one and not need it like I did with the angle sensor. Any help is greatly appreciated.
RE: Honda Rubicon Shift Problems 2008/04/09 05:56:07
I would clean the shift control motor ... Then initialize and re-test the bike ...
these are the tools needed to clean the shift control motor ..

Remove the allen bolts and remove the motor case (reach under the motor and hold the
spline teeth of the stator or it will come out when you remove the motor case ..

The magnets are epoxied onto the case make sure the glue hasn't seperated
and the magnets are in good shape ..

Remove the armature and check the commutator bars (as you see these were bad
before I cleaned them up ..

Check the springs ...

Install the springs and brushes back into the track they run on and
install the armature it's easier if there are 2 people for this step
1 to hold the brushes back , 1 to install the armature ..

Use a small screwdriver and apply a little grease around the rubber seal
and a small spot of grease on the bushing inside the motor case ..
(do a better job of greasing than I did) ..Then reach under and hold the
armature while installing the motor case (if you don't hold the armature
the magnets will pull it out of the brushes) install the screws ...

Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/10 12:22:24
Hey man
I just had my 2007 honda Rubicon fixed they put a new angle censor and then ran up under seat and coated it with clear selent so it could not get wet again and break. The part is about $80.00 and you can do it your self and fix the flashing you self.
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/11 09:52:15
Well I cleaned the control motor last night and re-installed it and still the same thing. "_",D1,D2 and ESP all flashing constantly as soon as you turn on the key. I pulled the code and still "11". Followed the flow chart all the way to the end and according to the book the ECM is bad. I ordered one today, it should be here by Tuesday. I'll let you know how it goes.
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/16 07:20:44
Got the new ECM last night, plugged it in and same problem. Still showing code "11". I tried to erase, wouldn't work, tried the initialization procedure, wouldn't work. I followed the flow chart for code 11, 3 and 7 and all came out fine. I checked the handlebar switch it checked out fine. Checked the charge on battery, checked frame ground and they're good. I'm planning on doing some testing the the combination meter next week. I'm kind of lost now. Any other suggestions?
RE: Honda Rubicon Shift Problems 2008/04/16 08:41:25
did you test the mode select switch, i've had a few of them go bad. another thing to check is the gear position switch.
Dirt Monster
RE: Honda Rubicon Shift Problems 2008/04/16 17:56:43
my dad was gonna buy a 01 rubi but when he went look at it, it had the same problem
Respected Member
RE: Honda Rubicon Shift Problems 2008/04/16 18:16:10
Does that year ruby have the start in gear feature?

If so you might check and make sure a brake isn't sticking and keeping it engaged.
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/22 18:28:50
I have a 02 Rubicon 500 and when I turn the key on sometimes it will blink all 3 of the D1 D2 and ESP.  It does not do it all the time and when it seems to do it i am moving at a good speed.  When they all are blinking it also Sputters in reverse and then will not shift in either drive selections.  Also when it is not doing that problem my spedometer will go out of wack and be ok for a minute then have wrong numbers and say all sorts of numbers then just stop working and say 0 so does anyone no what this could be?
RE: Honda Rubicon Shift Problems 2008/04/23 10:16:22
rubicon 500, i would get the speed sensor checked out might be your problem
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/23 19:42:37
would that cause it to not no which shift mode or gear it is in also?
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 12:28:50
Rubicon 500, when it flashes like that it is indicating there is a problem and a trouble code would have been stored in the ECM erasable memory. Stop and do the code retreival procedure and see what code it gives you and troubleshoot from there. You can either revreive the code now as it will be stored until you erase it or wait for it to flash again and then do it to get the most recent code.
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 18:06:15
how do you retrieve the code?
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 18:18:19
Rubicon Hondamatic Code Retrieval

1. Put the gear shift lever in neutral (be sure the neutral indicator comes on) and the ignition switch OFF (vehicle at a stop).
2. While pushing the UP and DOWN shift switches (ESP) simultaneously, turn the ignition key to the on position.
3. Release the UP and DOWN switches immediately, then at the same time push both the UP and DOWN shift switches again and hold form more than 2 seconds.
4. The problem code is displayed by a certain number of blinks “ - - “ on the gear indicator, which indicates the problem code by the number of blinks. If “N” (neutral) stays ON on the position indicator, the retrieval process was not correctly performed. Repeat the procedures from step one at this time.)
5. When the problem code(s) displays, release the shift switches.

You should see “ - - “ for approximately 3 seconds then off, then the “ - - “ should flash, once for code one, twice for code two and so on. The engine control module (ECM) can store two different codes. If your ECM has stored two different codes, the first code displayed is the most recent and the second code is the earlier code. Write them down.
To Erase the Problem Codes
1. Push and hold the UP and DOWN shift switches simultaneously for 3 seconds of more while the problem code is being displayed (i.e., “ - - “ blinking on the gear position indictor).
2. When the erasure is completed, the blinking pattern changes to the erasure confirmation blink.
3. Turn the ignition off.

Initial Setting Procedure
· After replacement of any of the following parts, perform the initial setting procedure below.
- Throttle sensor*
- Angle sensor
*Also, perform the initial setting procedure if the throttle cable is disconnected (i.e., car-buretor removal/installation, cable replacement etc.).
· The gear position blinks in Indicator Mode 2 when the initial setting was not made properly. Repeat the procedure from step 2.
1. Start the engine and let it idle about one minute with the sub-transmission in neutral. Stop the engine.
2. Make sure the gearshift lever is in the neutral position (be sure the neutral indicator comes on) and turn the ignition switch off.
3. Turn the ignition switch ON while pushing the UP and DOWN shift switches (ESP shift switches) simultaneously.
4. Release both the UP and DOWN shift switches immediately, then push and release the shift switches in the order of UP, DOWN, and UP. Do not hold the switches in).
5. A constant “ - - “ indication stays ON on the gear selector indicator. (If the gear position indicator shows a continuous “N”, repeat the procedure from step 2.)
6. Move the throttle lever to the fully closed position, then to the fully open position, and then move it to the fully closed position again immediately (within 10 seconds) after “ - - “ comes ON on the gear position indicator.
7. Check the control motor operation sound (the control motor should function at this time to adjust the angle sensor).
8. When the initial setting procedure is complete, the indication on the gear selector indicator changes from the continuous lighting of “ - - “ to the continuous lighting of “N”.
Code 1 - Ignition Pulse Generator system
Code 2 - Speed Sensor System
Code 3 - Gear Position Switch System
Code 4 - Throttle Sensor System
Code 5 - Angle Sensor System (Motor lock i.e., angle sensor, wiring, ECM, control
motor, motor transmission section, transmission unit)
Code 6 - Angle Sensor System (swash plate angle, sensor / wiring)
Code 7 - ESP shift switch system
Code 9 - ECM voltage converter circuit
Code 10 - ECM fail-safe relay circuit
Code 11 - ECM motor drive circuit
Code 12 - ECM CPU

You should try to get a Honda service manual for the bike, I got mine off ebay for about $20. Someone posted a pdf file of the whole manual a while back but I'm not sure which forum. I think I have it on my computer at work but won't be able to send it to you until Tuesday.
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 18:27:03

Here's the link to the manual, not sure exactly what years it covers or what year it was written. Mine is an '01 and it seemed slightly different but it should be helpfull when you start troubleshooting.
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 19:00:40
I recieved code 2 which on the instructions you sent to me it says the speed sensor which i can see that may be because when before the D1 D2 and ESP start to blink the speedometer stops to work. It had the same code for both of the readings.  Do you no much about the sensors and how much they cost?
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/25 22:31:42
Go to Bikebandit.com to check on the price, they're usually slightly cheaper than the Honda dealer. Check the link for the manual on how to troubleshoot for Code 2 and test the senson. It may not be a bad sensor but a bad connection, broken wire, etc. You don't want to spend $ on something you don't need. Trust me I've allready bought an angle sensor and an ECM and I'm still not riding yet. From the best I can my problem is in the control motor so I'll probably order one next week and cross my fingers. 
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/26 17:45:01
cool thank you for all of the help ill let you no if it fixes it
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/26 18:54:53
i went and found the speed sensor but now my machine is pulling up code 10 and i cant find it on bikebandit.com any help on what this one might be?
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/28 22:01:52
I jumped 12v to the control motor and it turns, I put it back on the bike and jumped 12v to it and I can hear it turning but the display just keeps flashing. I still get code 11, I clear it but the initial procedure won't work, the control motor does nothing when I try it. I've went through the flow chart for code 11, 3 and 7 and they all check out fine. I've allready replaced the angle sensor and ECM. I'm stuck?
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/04/29 14:01:11
have you checked you gear positions switch? that could be your problem. On my 02 Rubi i am getting code 2 and 10 so im bringing it to a dealer to see if they can find the problem with code 10 code 2 is just a easy speed sensor but i would check the gear position switch.
o7 rubicon
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/09 00:32:00
my 07 has the same reverse problem brand new with.9 km on it.
o7 rubicon
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/09 00:33:01
i dont knowwhat to do its very frustrating
Rubicon 500
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/09 13:53:02
it should still be under warrenty but my guess for you would be an angle sensor or just a bad machine so i would just bring it to a dealer becuase it should still be covered

o7 rubicon
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/09 22:53:03
mine only has a problem in reverse, until i went for a ride last night and now d1 d2 esp flash 4 times and its like a limp home mode. i have a recall notice for a throttle position wiring harness. i live in northern b.c. canada 4 hours from the next dealer. the dealer in town has no mechanics, one has a family problem and the other one cut offhis fingers or something. i am going to call Honda Canada on monday. does anybody know how to reset the flashing codes to see if they come back again
Road Hammer
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/09 23:23:28
Hey just ran into the same problem last weekend i have an 07 Rubicon and it was doing the same thing as yours but i was flashing a code 5 are you sure you red the code properly i resolved the problem by blowing my angle sensor out with compressed air ang filling it with dialectric greese this didnt solve it all but what did it was resetting the computer.
What i would suggest is put it all back togeather the way it was and reset the computer you will hear the angle sensor realign itself
1. run the motor for 1 min
2. tunr it off
3. place in nuetral
4. hold up and down shift at the same time
5. turn the key on and let go of buttons it should flash ;-;
6 . press up shift and down shift in that order 2 or 3 times
7 . open and close the throttle 2 or three times
you should of herd the sensor line up by  step 4
Outlaw Extremist
RE: Honda Rubicon Shift Problems 2008/05/09 23:26:44
Here is the procedure for retrieving and erasing problem codes on your Rubicon.
Outlaw Extremist
RE: Honda Rubicon Shift Problems 2008/05/09 23:42:50
Here is the test procedure for problem code 4.  Start by looking for moisture in the TP sensor connector.  I had a brand new Rubicon the other day with problem code 4.  The problem turned out to be a TP sensor connector that was improperly clipped in from the factory.



Greg Loflin
Mud Master
RE: Honda Rubicon Shift Problems 2008/05/11 22:46:45
I have a Rubicon, had same problems, put on a new angle sensor, seemed to fix it for a while. Problem came back, got to checking the swash plate motor, it would check good, sometimes, sometimes not. Tried cleaning it, same problem, replaced swash plate motor, been ridin' ever since.
o7 rubicon
Grass Hog
RE: Honda Rubicon Shift Problems 2008/05/22 21:44:20
i think i found my problem with reverse. my quad was brandnew and assembled too quickly and the linkages were adjusted wrong. ive set them up and now i rode 2 days and no problem with reverse.
Grass Hog
Re: RE: Honda Rubicon Shift Problems 2009/04/26 22:42:42
Great Question. I own a 2007 Rubicon Canadian trail Ed. And went through all the problems in the above posts, took it to the dealer and they tell me its my ECM, and dealer wants 480.00 for a new one. My question is if i go buy a used ECM will any model ECM work or do i need a certin one for my Model due to it being the Cdn Trail Ed with the GPS ???? Any help would be Much Appreciated. Thanks!
Trail Rider
Re: RE: Honda Rubicon Shift Problems 2009/04/27 07:16:13
the GPS is not connected to the ECM if I am correct. I believe you can get any ECM compatible with a 2007 Rubicon and you will be good to go.

Thanks for all the info guys. My '05 Rubi flashed and sputtered one time, but, knock on wood, it has not done it again. If so I now know where to look for solutions