I am only familiar with the 6R75 transmission (used in 07-08 Expeditions) and it uses an internal TCM in the case that communicates with the ECM. The 6R75 is all solenoid based with no bands....I replaced the Torque Converter in mine with a reman because it lost lockup so I had it out and apart to replace some solenoids/filter/bridge seal stuff as well. In 2007 Ford started to use the new ECM setup so it would be more than a TCM to make it all work. The 6R75 is quite an improvement over the 4R75 as far as I can tell...the 6R75 starts in a lower gear ratio for better off the line power and ends up in a taller ratio on the thruway for better fuel economy. It also is always in the correct gear when towing my boat. Cannot comment on the 6R80 though.
If I had a 2nd gen with a trans issue I’d personally just rebuild the 4 speed, less hassle and it will work as intended. Unless of course you were building a modded up performance truck go for it....other than that the 4R will keep everything happy without electrical gremlins.