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After doing as much forum stalking as I could and getting bits and pieces of what I need. I finally decided to do it right and ask the professionals directly. Here is my known issues;

Picked up a 2006 Honda Rancher 400fa AT. Had been sitting for a year. PO said that it stopped shifting and would only stay in first.
After I cleaned out the carb and replace the battery it started right up and runs perfect. But still won't shift in ESP or Auto mode. Magnets in the shifting motor were shot and wire was shorted out. Also, the Shift motor fuse was blown. I replaced both. I have tested the angle sensor and throttle position sensor with a voltmeter and they are both within specs.

I tried to Initialize the ECU and get the shift motor to cycle the swashplate and the "--" blinks. When I move the throttle back and forth nothing happens. I have tried numerous times and still get no response.

Sorry if I haven't put things in the perfect order or used the wrong terminology but not only do I want to fix this quad; I also want to learn.

Appreciate any and all help. Thank You in advance.
 

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