Injectors at the TBI are a disadvantage at throttle tip-in compared to near valve port injection. With TBI, additional fuel is proceeded by the mix already in the runners and plenum. While large tip-in enrichment helps some, much of the extra fuel is wasted by wetting the intake surfaces, resulting in less control of enrichment decay. Dyno numbers may be as good, but drive ability and fuel economy suffers.
MS2 and MS3 have different microcontrollers and embedded firmware. I am not sure about the PC based tuning software.
