If you check the link I posted above, it relates specifically to engine swapped vehicles. As long as the original diagnostics and emissions control systems are left intact and 100% functional on the new motor, it sounds like it would be passable.... at least that's how I'm reading the info.
Edit: There is also a lot of caveat wording there, relating to ensuring the engine is emissions certified to the same year as the original vehicle, etc. It is a very fine line you walk in CA. Be informed before making any decisions.