Obviously, I don't know the system in California, but here in Ontario, the provincial government is starting to enforce existing laws regarding emissions equipment compliance much more strictly than they used to. A local enthusiast was pulled over by the provincial Ministry of Environment enforcement people in his 1932 Ford street rod and they inspected the small block Chev engine in it. They were able to decode the engine using the casting and stamping numbers, and determined that the engine was originally installed in a mid '80s Chev truck. The owner was cited for no EGR, no evaporative canister, no thermostatic air cleaner, and one or two other offences, and he ended up retrofitting the emission controls to the car. Here in Ontario, the rule is that the vehicle must have the proper emission controls for either the vehicle, or the engine, WHICHEVER IS NEWER. The Ministry people have access to manufacturers records, so they can determine the original use of most engines. If you want to drive a vehicle with few or no emission controls here, you have to have an older vehicle (pre 1970) with an older engine (pre 1970).
I've modified the engine in my 1984 Monte SS (yes, I know its a Chubby), but I've used CARB certified parts wherever necessary, and its made quite an improvement. I'm not afraid to drive or show my car, because I've kept all of the original emission controls intact and functional. Like I said before, I don't know exactly what the regulations are in California, but if you swap engines within the same engine family, and make it work efficiently (as stated above), then I can't see why you can'y have your cake and eat it too. Just my $0.02.