We talked about this in the really long Apex thread. My conclusion was the best way to go in Ca. is to go SB100 with new VIN.
Since it isn't a replica of another car, you get the smog requirement of 1965 and can basically do what you want with exhaust, turbos, engine swaps, etc. If you use the title of the original car, you must use the same equipment that it had or risk a smog check fail.
At least that's the gist of what I recall about it when I looked into it.
As for safety, I don't believe they look for energy absorbing zones and such (otherwise how would Cobras pass?). I think it is more that it has seatbelts, things are permanently attached, etc. Basic stuff.