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Okay so this is on a 500 Rubicon 2003. Has new angle sensor new shift motor and had to change out the display as well. It shifts 1st 2nd and 3rd gear just fine once in 4th you can hear the gear that the shift motor operates hit the end of its travel and locks up. Now I would say this is because the initial reset/relearning procedure needs to be completed so that everything will line back up correctly however when attempting to complete this process you can hear the shift motor run for just a few seconds and then stops which is not allowing the initial procedure to be completed. I have taken the motor off and checked the gear and it is locked usually have to get a screwdriver and release it. I have counted the rotations of the gear and put it at the halfway point which is 6 rotations and it still will not reset nor shift past 3rd. Just to try it I had a used computer laying around so stuck it on and tried to relearn it and still no luck. I'm to the point of taken it out and splitting the case but just wanted to get another opinion before doing that. Sooo do anyone of you all have any ideas or suggestions before I tackle this task and this customer has to pay for a new transmission. It almost seems to me like the rear swash plate is stuck but I'm not to sure.... HELPPPPPPPP
 

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When it is locked, I would assume it is at the end point, or 5th gear. Locking up at the end of travel is a common problem.
Have you tried putting it at the start point, which you say is 12 rotations?
 

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From sticky post:
If you change oil and it has lots of crap including metal in the oil the hondamatic motor side swivel swash plate bearing is toast.

It is possible that the number of rotations is supposed to be about 20 or so, but no way to verify without a working Hondamatic. If we assume that 12 rotations is normal, then the problem is some part that locks up at the end of travel of the shift shaft, a common problem - see picture.

Maybe a weaker shift motor would not cause the end of travel lockup. Or the shift motor is getting too much voltage. Try disconnecting the voltage regulator and using a depleted battery putting out only 12.0 volts or so.
HondamaticShiftShaft.jpg
 
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