I know a lot more now than I did in 2010 regarding the differences between '94 and '95 4L60Es. Based on what I've seen with the 4L60Es and in TunerCat, and some work I've done, it looks like GM design was planning on introducing PWM control of the TCC apply rate the whole time, but perhaps they didn't quite have it ready for the '94 model year. The reason I say this is because the valvebody casting number is the same for '94 and '95 but changed in '96 for other reasons (manual valve, 3-2 downshift solenoid).
It looks like what changed physically for '95 was the addition of the PWM solenoid, a different spacer place with holes to provide AFL to the solenoid, a different pump labeled "PWM" on the outside, and a changed TCC apply valve in the valvebody.
So if you're putting a '94 trans with a '95 or '96 PCM, you should be able to do it all in the programming. You would turn off the TCC apply solenoid error (I forget which one it is at the moment but it's labeled in TunerCat), then copy over the '94 TCC apply and release tables (this step might be optional but I never had the time to experiment).
Obviously this is not for someone who has no experience with TunerCat, but it can be done by someone who knows their way around.