OMFG! I typed this longass reply and when I went to post it asked me to log on...so I lost it all WTF! ARGH! So now I gots to do it all over again. Sorry had to vent.
Essentially any tranny that was offered with a S series engine will bolt up to it ie. Celica, MR2, Alltrac, Altezza...some are bolt-ins others require modifications. In theory a MR2 tranny will work and is the stronger transmission to use, however this will require you to swap a few parts from your GTS tranny as well as having to make hybrid axles. I know because this is what I have setup on my 88 GTS(3sgte swap w/e153 lsd), but it isnt cheap nor for the faint of heart, however the rewards are +++
Apperenetly the syncros are not the greatest in these trannies and one would be led to belive that they were made of plastic...First I would try and diagnois what it is exactly wrong with your current tranny and fix that. I hope you are using ATF fluid and
not Manual tranny fluid cause that is what you are suppose to be using in this model tranny. Try adding a transmission additive like AMSoil or Lucas brand oils. If having to replace your transmission is the only alternative you could have it rebuilt $$$, or source a low milage unit from a junk yard or import shop$$$, but you are not granantied that the syncros haven't gone bad in them either. 86-99
JDM Celica's that came with the 3sge motor will work.
Or you could purchase my 2nd gen GTS tranny with your chioce of clutch and pressure plate (MR2 or GTS) and freashly rebuilt drive axles using manual tranny lube for cheap and have piece of mind...
-Daniel Lamoureux