I have found a very nice 91-93 MR2 5sfe manual tranny for my st185 3s will it bolt up ?

yes it will bolt right up...
i dont knwo if this was what i had read but i believe deph recomended upgrading it because its not built for the power and might not hold for very long...
how much work are u planning on doing to the actual motor as far as power output?

idk yet ill eventually Do work on it like rob and big because i dont think i will be like some people who do the swap and then sell it once i upgrade tubo's ill upgrade tranny's but that wont be for a while lol