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Found it. Looks like a pretty immensely complicated process! I really hope I can pull it off correctly.

Could someone please tell me where to find the directions for the reinitialization process? 30 minutes into reading the manual, my phone crashed.

Extremely frustrating.

3 hours ago, wheelsquad said:

The computer I'm on most of the time has Google Drive access blocked, and yep, pain in the rear to look on phone but that's what I just did. Pg 24-32 says to check the connections, and I can vouch from experience that one time mine got all wonky with shifting and error codes, and a loose connector was the cause. Good thing to try would be to take every connector apart, clean, and re-assemble with dielectric grease.

Actually now I’m second guessing myself. I can’t remember if it was 12 or 13 blinks…but I could have sworn it was an ECM code, not the ECM drive motor.

it was well over a year ago since I’ve even had a battery in it. Luckily I kept the battery charged.

when I get off work, I’ll check.

I did clean, and grease at least some of the connections, but I am unsure if I unplugged everything. I will go over it again when I have enough time to be thorough. Thanks to everyone taking the time to give their input. 
does the ecm need reset after changing the angle sensor?

I did change the sensor but am unsure exactly how to reset.

My ex bought a used 06 Rancher 400AT, that was used for one week, until it stopped shifting.

Now this quad has been sitting in my driveway broken for two years, and I am sick of looking at it! I replaced the angle sensor, tested the regulator, cleaned and greased all the plugs…etc. Nothing has changed. Does the ecm need reset when changing sensors? If so, where can I find the correct procedure? It flashes 12 times. It chugs in reverse, and won’t shift out of first.

One atv mechanic worked on it for a few hours, but didn’t seem interested in returning.

Another ATV mechanic from an actual Honda dealer told me it’s not worth fixing….

I am personally running out of Ideas…I do believe that the ecm is bad, but don’t really want to spend the money if that’s not the whole problem.

Now for the question of the hour…Does a Honda engine/trans exist, that is manual shift, and feasible to mount to this Rancher frame? I mean this Rancher looks brand spanking new…but
I’ve had it with this overly complicated pos design…and am willing to throw $2k at it to make it reliable, especially looking at the price of used quads.