RE: superchargers
basically the supercharger forces air into the crankcase, and its near impossible to get enough fuel to go with it.
on a nitro 4 stroke they may have some grounds to work since there is actual valves that can close and create pressure giving the carb enough time to inject some more fuel, however to the best of my knowledge they rob just as much HP as they make and cause over heating, as well as reducing the amount of lube in the lower end
2 strokes are simple and like to be left simple (K.I.S.S rule, keep it simple stupid applies to almost everything RC)
a nice header and tuned pipe are best.
macs tuned pipes are good and from what i understand hpi headers are good. if you've got a dremel match the size of the exhaust exit on the motor to the header, or match the header to the exhaust ports. (port matching).
as far as motors. if the boat you've got originally had a .12 or a .15 try a .18 since they all mount in the same space.
if its a larger size than that, im not really sure what motors share similar lower end sizes.
also playing with your prop can help you gain speed, as well as polishing the surfaces that contact the water (strut, rudder) which will reduce drag.