I want to make a comment about something that was said earlier in the thread. If I'm repeating someone else's comments, apologies.
So this is regarding parasitic losses of the supercharger. Yes, it's true that in this project there is no "new" part that gets added to the motor, but when we talk about the supercharger overhead, we have to remember that it's no longer a 500 -- it's a 250 single now with a supercharger that happens to be driven directly instead of a chain or what have you. But the fact remains that some of the energy the single will produce, must go toward driving the supercharger (other cylinder). Yes, there are some efficiency gains in terms of better coupling of "engine" and "supercharger", but physics tells you that there's no free lunch here: the air still has to be compressed in the supercharger and it takes a certain amount of energy.
On the plus side, thermodynamics tells us that the supercharger cylinder will generate some heat because all it's gonna be doing is compressing air at 2-stroke rate. That means that while there probably won't be the same temperature parity across the head gasket as you'd see on a stock GS500 motor, it won't be as though one side is hot and the other cold. So, while another energy loss, this may help some with the gasket and head longevity.