Count Down to Extinction (besides not having a movie tie in with its name) was largely the same as the ride is today. However during those days when the ride was new almost all, if not all, of the effects were working...many of which have simply disappeared or been altered since. Some that come to mind are the Petrydoctal (or Teradoctyl, not sure what the actual animal is), the Compies, and some cool laser effects in the first time travel sequence.
It is also agreed that when it was CTX, the ride was distinctly more bumpy, fierce, and generally more thrilling...very similar as to how when Mission: Space first opened the G-forces were more intense but were toned down later.
Also when it was CTX, they actually let you see the whole preshow and didn't just keep shoving people into the preshow rooms in the middle of it although that is more of an operations issue than an actual change.
Finally, as far as I can remember the clip of the dinosaur in the preshow was a bit different although for the life of me I can't remember how, it was similar to the current one though.
Hope this helps a bit. Let me know if you have any other questions.