All hypotehtical, but

If one wanted to make a race car based around the s2k engine and drive train, but build the rest of the car from the ground up, what racing groups/classes could one compete in?

 

I'm thinking Winston Cup

 

You would really need to ask the sanctioning body you want to go with.
SCCA for example(as far as I know) has only classed the S2k in T2 which is real close to stock.
But they run Boxster in GT2(tube frame,glass bodies,...)
So if it hasn't already been classed you can request the SCCA to do so and build yourself a GT2 S2k.
I think the motor is to big for 'Sports Racer' and the Formula classes all run the same motors (Ford, Mazda, or Toyota). I only know about SCCA. ALMS,NASCAR,...?

 

I know the question was hypothetical, but there are much cheaper ways to go racing than picking a high dollar engine with a limited after market as a starting place.