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While the ce light is flashing remove your jumper/paperclip/whatever and it should clear the codes. Attempt to pull codes again to verify they're gone.
Well I got the new PCM today, drove it around and nothing changed which was a little upsetting. But when I scanned it I finally got code 634 for low/high voltage to MLPS. I crawled under the truck and blew compressed air into the MLPS connector, cleared the code, drove it around the back roads for a good 30-40 minutes and it only shifted hard once when I was hammering it up a hill. It still shifts a little late, but overall it's driving great and the code hasn't come back so far, glad to finally get some resolution with this pos.
The older ones had a harness inside the trans that would get contaminated with trans fluid and cause all kinds of problems
The newer ones experience the same thing, but it is usually just the little connector that goes through the trans case that gets contaminated, and needs to be replaced
Blowing it out and cleaning it all up, (followed by road tests and code checks) is a decent enough test
Good luck