I have been following several threads about non-shifting Rubicons while trying to fix mine. No luck so far. Any help is appreciated.
Here's the background: It's a 2003 TRX500F Rubicon, went blasting in some deep mud and water (River Ranch, FL); had to bail out from a bottomless pit; the bike floated for about 10 minutes while towing it out; hit the starter and after 10-15 seconds she fired up and spit out all the water; ran great for several more hours, then after stopping for a beer break, started her up to find she will only run in first gear.

So....I have performed the diagnostics and the Gear Shift Indicator flashes 6 times which equals 'Angle Sensor Output Voltage is out of specified value'. Ordered a new Angle Sensor ($48.00), no joy, same thing. Next, I performed the Initial Setting procedure for the tranny; Sub-Trans in neutral, Drive Mode in D1, ignition On while pressing both UP and Down switches, release switches then press Up, press Down then Up again, press throttle wide open then relaese. At this point, I should here the control motor turning for approx. 4 seconds to adjust the new Angle Sensor. It doesn't, I only hear an initial 'Click' coming from the control motor.

Other strange things; while the motor will run fine in first gear going forward, when in reverse the motor chokes and hesitates. I have checked all electrical connections including main controller (clean and dry). When the key is turned on (without starting motor) the gear position indicator display begins a constant rapid flash.

Trying my best not to bow down to the local repair guy. What am I missing??

 

Did you check for water in the oil after you drowned it? Don't the engine and trans share the same oil? Maybe you gunked up the transmission from dirty oil?

 

I posted the following on another thread, I hope this helps you out.

I have the Rancher AT so my codes are different than yours but they all have the same piece of chit Hondamatic Transmission. Angle sensor is a good place to start, it is easy to test and only about 40 -80 smackers if that is the problem. Inside the Transmission control motor (shift Motor) there is a worm screw that runs 22 turns out and 22 turns in. When it hits the end it locks up and causes bad chit to happen. If your angle sensor checks out and your shift motor checks out you can take off the shift motor and run the worm screw back to dead center. slap it all back together and perform the initial setting procedures without step 3 (pulling it 5 ft forward). I am not sure if this will help you it being a different machine but I am 600$ into my tranny now and after 3 months in my garage 4 weeks in the shop a control motor and a angle sensor I called the engineers at Honda and that's what they had me do. It seems to be working fine so far.

 

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I am very happy that I bought the standard shift foreman! I will never have to worry about problems like this!