I don't live in cali, but if you want to pass emission you need to replace some other components with USDM components. If you notice the power output for a JDM 2JZ is lower than the USDM 2JZ. This is because of different ECU setup as well as cams, turbos, injectors and intake manifold (for brakebooster line and EGR). You might be better off sourcing a 2JZ from a USDM supra, but those are insanely hard to find.
I would have smog the car first then do the swap, but if you already have it swapped and need it smog. Most people in cali slip a few bills to get it smogged illegal. Poster above me true if you want to pass smog with a 2jzgte swap its best to source out a USDM 2jzgte. California has the strictest(?) emission rules it is ridiculous.
if have somone that will pass visual. you can try and pass the sniffer on the jdm engine, thats what im going to try and do. probably throw a new cat on it, pour some crap in the tank to cool that combustion chambers