holy bajeebus...I could go on for quite a while about options...all really pending about how serious you want to go with performance?
ultimately how much power do you want from the car? That will be my first question
Three main roads assuming you are looking at a 99-01 RS...other models my suggestions would vary a bit.
1. Factory turbo engine swap doing lots of wiring
2. Turbo the SOHC EJ25 and run plug and play hydra
3. install factory turbo engine (or pre-built one pending power goals) and custom plug and play hydra to make it work...yes, Andrew can do it...you can even has a AVCS board that'll plug and play in a RS

All can make great power but some easier than others...personally choice 3 is what I'd suggest having done the other two. The SOHC will cap your power goals becuase of cams and head flow. Highest I've ever seen was one I work on making 460 lb-ft of torque on our mustang dyno (540'ish on a dynojet). Wiring in a factory engine is a lot of labor and PITA. Pre 96's are even more intensive and difficult. 96+'s aren't that bad but time consuming.
As for drivetrain, let me know your power goals...I'll let you know tranny and diff suggestions...

Put simply, let us know what you want to get from the car power or performance wise...that'll help to narrow my suggestions