your running a supercharger on a stock airbox??? why??? if just the airfilter made a difference think of what replaceing all that stock piping would do!!!
I have yet to see any conclusive evidence that it makes any significant difference. There have been a couple of dyno tests which have shown 1-2 hp delta's (sometimes negative), which may simply be the error tolerance on the dyno. On the other hand, improperly maintaining a high flow filter can lead to crap getting into your engine. If it made even 3-4hp difference, I'd do it, but I don't think it does, so I'd rather not take any chances.