Welcome to the forum.

This one sounds interesting. Your diagnostic tests seem to have created as many questions as answers. First and foremost is that it appears the ECM believes it is seeing greater than 200 rpm difference between engine speed and input shaft speed. It sounds like you've attempted validation testing to confirm the issue but the results were not helpful. Here's a few more answers.

1) The four wires from the distributor are labelled REFerence, EST, Bypass, and signal low. REFerence is the white wire and it provides a square wave signal from the module to the ecm. EST is the purple / white wire that carries the timing signal from the ECM to the module. EST is also a square wave when the ECM is commanding timing. The Bypass wire is tan / black and you will read 5V on that wire when the ecm wants to control timing or zero volts when the ecm does not want to control timing. Black / red is signal low, a dedicated ground between the module and ECM. The wave you're describing sounds like ignition secondary pattern. Ignition secondary should not show up on the wires between ECM and distributor.

It is possible to calculate rpm using the measured time between the start of two of the square wave pulses then doing math. 720 / number of cylinders / time measured * 60 should give RPM.

With the TCC locked I would expect to see the same RPM between the engine and the ISS. With TCC unlocked I would expect to see the difference between ISS and RPM vary from very high under load to almost zero when coasting. If I suspected actual slip I might try locking the TCC then watching for the difference in RPM between ISS and engine to behave somewhat like unlocked TCC behavior: more slippage under load and nearly zero when coasting.

We used to have a guy here that had a bunch of 4L80E knowledge. I haven't seen him post in a while. But as I remember the new "black" force motor was introduced into all 4L80E in 1994 while older models used the "silver" force motor. I do not have a chart that links your EPROM code to force motor types, but you need a prom that provides 614 Hz control of the force motor.