How about a stimulator (virtual engine) for the stock ECU?
1) Install stand alone ECU of choice.
2) Tune.
3) Leave the stock computer hooked up to the diagnostic ports on the car (anyone interrogating the car would plug into the OBD port), since the stock Denso computer's wires leading to the sensors and actuators on the engine have been replaced by connectors from the stand alone, hook them up to a box that tells the stock computer that everything is just great - a digital lobotomy.
That way the car can be run using a stand alone computer and the stock computer can spit out appropriate code for emissions testing.
My inspiration for this idea is Megasquirt. Bowling and Grippo suggest the fabrication of a stimulator box to test their home brewed EFI or EEC modules, so what would it take to make a similar stimulator (virtual engine) for the much more complicated factory OBD II computers?
Mike