Well it shifted gears, that's progress in my book.
I replayed the logs a few times, and the turbine and output shaft speeds looks pretty solid. Didn't notice any jumps or drops, so guessing it's TOS jumping around is noise related. The 5v patterns looked good on bench, so would like to compare on a truck if ya can scope it. There is a 220ohm pull down resistor in that circuit, as the other two output lines. You can remove and see how it acts. I haven't tested these boards wihout, but thinking we start there.
Also we can try powering the board with 12v rather than robing power from the TCM ref line. I tested for a good bit with 12v power, and against theE38, but not sure how that TOS line signal looks with other nodes involved. I'll send ya a pic of jumper to de-solder, and then we can power it off that extra terminal and see how reacts.
Let me know if you have any analog scope handy, and bet we can sort it out pretty quickly. Other codes, I think we can adjust with those pots.