Can't comment on the 3 speed trans, can you provide some more info, like who makes it?
Four storke engines produce less power for a given size than 2 strokes. That's just the nature of them... You'd have to go with a significantly bigger engine to get power on par with a 2 stroke. 4 strokes should respond well to turbo or supercharging.
One other thing to consider though... even if you manage to get a 4 stroke up to the horsepower level of a 2 stroke, it's going to be making that power at a MUCH lower RPM, you might find it hard or even impossible to gear the car appropriately unless it's been designed around a 4 stroke powerplant.