Do not waste your times with cams. 4.6L cams cost a ton and offer very minimal gains.
Don't see or know your current mods, but go. CAI, L/T's, h-pipe, catback, 4.10's, MGW shifter, and a tune.
Don't waste your time with a throttle body either. They are good for 450-500RWHP. I've seen 96-98 and 99-01 Cobras lay down 530RWHP with stock throttle bodies.
IF you can afford a superchargers, that's the way to go. Make sure you have a good clutch before the install of a supercharger or L/T headers.