I am curious as to your conclusion #1 is close to the knock sensor. The knock sensor is in the block drain on the passenger side, just in front of the starter and sits between cylinder 4 and cylinder 6 right above the oil pan rail. The only thing I can think of close to cylinder 1 spark plug would be the coolant temperature sending unit for the gauge that is between and above cylinder 1 and cylinder 3 spark plugs.
The transmission shift points and lockup are all controlled by TPS and vehicle speed.
Your compression test seems a little low to me, but my test method may have been different, my gauge is different, etc. What I am looking at is consistency and low cranking pressure in two adjacent cylinders. These engines often blow head gaskets between cylinders 4 and cylinder 6 and sometimes between cylinder 3 and cylinder 5 in a way that they will not leak or burn coolant, just run poorly. Does not appear to be an issue with yours though.