There are 2 things you can do to pass emissions.
1. Run a piggy back ECU to tune with. At least with the AEM FIC, you can retard ignition timing based on when the stock ECU fires the plug (no ignition timing advancement unless you turn the distributor to induce an advanced state across the map), modify the duty cycle of the injectors (can run essentially any injector you want since duty cycle is adjustable), have a 10+ psi capable map sensor, and modify the O2 signal to the OEM ecu. By using a fully functional piggy back like the FIC you can pass emissions and run a fairly nice setup. Problem is finding someone capable of tuning this, and dealing with the tricking of the stock ECU voltages.
2. Run any programmable ECU you want and swap out everything that is related to the control of the motor when ever emissions time comes around. Open up the wastegate and make sure the cat is on there. Gotta change injectors, O2 sensor wiring (if you wired a wideband on pin C16 on the ECU which was the original narrow band line [depends on which pin the ECU uses for the wideband]). Then pass the motor through with no check engine lights
It also depends on what your state requires. In NY and CT at least, if your ECU cannot interface with the OBD2 system that the emissions shop has, instant fail. They don't even do sniffer tests anymore (the last couple times i've gone), just OBD2 scanning.