So here's what I've done, that I remember to date
Put known working shifter controls in. Quad had controls taken apart and missing pieces to find shifting issue. I verified that these new to me controls do work, and have continuity when buttons depressed. Also jumped the pinouts in the connector to bypass the controls, still nothing. Black orange to either wire
Followed diag for wiring in honda manual. Checked most if not all wires that work with the es system. Only wire I found that wasn't right was the grey black wire going to CM. No continuity with ground with the plug connected, key on, and in nuetral
Speed sensor tested. Has correct input voltage. And reference wire outputs 5v and speed is recorded on CM
Replaced rectifier with known good rectifier
Replaced angle sensor with new oem honda sensor. Original tested good
ES shift motor spins with 12v, and has been cleaned inside no damage
All connectors in harness are dry, with absolutely no dirt inside. Also checked over the whole harness for damage, or wire pinches
Swapped ecus. One ecu is oem original. Another is Rocky mountain new oem. Both 771 codes. The old one has a steady neutral light. The new one has a flashing constantly neutral light. No codes. And no codes are retrievable.
The time on the CM resets after about a day even though the battery is being maintained at 13v+ constantly Edit: I found this to be wrong. I unplugged the CM about every day because I work on it every day. Killing the saved time.
Swapped batteries with known good battery
Tested all the fuses. They all tested good but I replaced them all anyways.
Gear position sensor records every gear on the CM and tests out good as well
Checked and verified grounds and battery connections
Voltage to ecu is battery standard voltage.
The only things that stand out to me is that the grey black in the CM doesn't have continuity to ground. They both have to do with the CM and I have not been able to swap that out yet, being I don't have one available. Akatv you mentioned these two things before.
Edit. Grounded the grey black wire just now and I hear a click from the ecu and the gear indicator goes blank. So I'm assuming now that I have a bad CM