Even in California I believe you match the smog equipment to the engine and car whichever is higher. Since you would be replacing your Boxster engine and exhaust with Porsche Carrera engine and exhaust of compatible/comparable year - it stays smog legal.
(caveat: I am a former Californian and have no legal training)
I haven't heard of anyone attempting a non-Porsche engine, but I have heard Audi has engines that mate well to the Porsche shared transmission. A Carrera engine will tromp a 1.8TT Audi engine so if you are looking for more power, the 3.4L is the way to go.
Read the archives and hang out at the Boxster Racing Board
http://www.iq.dynip.com/~racing/index.cgi/index.cgi?
and listen to them comparing notes on ODB codes, air intake questions, etc. This is not a job for the timid. No real good dynos yet. Engine dynos should be very close to the Porsche 996 that donated the engine.