What transmissions can I use
 

I was wondering if I could put a newer model engine and transmission into my 03 mini cooper s and what would it take

You can, but it will cost a good chunk of change because of the items you'll need to replace. Is there any specific reason as to why you don't want to put the same engine and transmission into it? The W11 engine in the R53 is a good engine. The Getrag 6-speed is also a good transmission.