As I recall the engine move was to enable modifications to the steering rack and to allow for the install of the gearbox. The suspension mods were done to improve the road handling and judging from experience it's certainly worked.
One thing that hasn't been pointed out is the the current SS engine won't be the one we see in production. SS had developed one of 2000 engine for a client who no longer want the engine. So guess what, this new lump will be exclusive to the M3W.
Seems to be very good; and one would expect that they had to do several changes, as you said for the gearbox etc. So it's more or less a completely new design it seems. Personally I’m happy that they ended up with S&S and not Harley (there would be endless questions to the owners about 'do you have Harley trike' etc.; and everyone plus dog seems to be riding a Harley).