I've been lurking around reading as many threads about transmission swaps as i can stand. what transmissions models are compatible with an 03 base cooper?
i've heard CVT (sucks), Midland (sucks), Getrag (???) and i think there was one more.

i'm trying to learn as much as i can before i have to put my cooper under the knife.

 

CVT to CVT.
Anything else is a big project...needs a donor car (to be done cost effectively, a rear ended totaled car, that with a good drive-train), computer,wiring harness and lots of parts. IMO if you don't plan to to provide the labor yourself, just keep the same type of tranny as the car came with...the shop labor $$$$ and no manual to do it will break the bank.
The r50 with a 5 speed can be modded to take a r53 6 speed, but the gearing is a bit off for it..it works though. Still needs lots of parts.
The midlands 5 speeds vary a bit...some were good, some bad...newer seemed to have better quality parts...and when not driven aggressively, many go the full life of the car....