I suspect that the hardware is the same, or very close. But, the S4 has a different throttle position sensor and different injectors than the air-cooled bikes, so it may be different HW from the other Monsters due to different resistance values of those parts. Likely the connectors are different too. I don't imagine the M800 and M1000 are all that different hardware wise, so I don't see a need for different part numbers, although maybe it just covers the maps that come on the CD/software.
you're right on track speeddog... i'd recommend checking the spare-parts sheets for the bikes and compare part numbers for the injectors and throttle position sensor (referred to as potentiometer in the parts sheets). if they're the same, you're gravy as that's where the PCIII connects to the bike.