I don't personally know of anyone that had great results when using the individual pods... my uinderstanding is that you'll end up with a big flat spot somehwere.. and maybe worse, unless you really get it right.
Also, remember that individual air pods will be a problem if you get caught in the rain; even WITH my airbox (drilled with 20 1/2" holes), there are times when i'm out on the highway, get caught in a heavy shower... and the bike will start to cough and kick from water getting in.. and that is WITH the airbox. i can imagine it could be much worse with pods. Still, they sure are easier to get on and off.
It depends on how you want to ride the bike. If you're just looking for local stunting or dragstrip use, open 'er up all the way.
But if you're thinking of doing any open road traveling at all... better stick closer to stock. And that includes jetting... I think you'd find a Stage 1 kit much more practical and friendly than a fat Stage 3, where your powerband will be more limited and your fuel economy will suffer.
And while I'm at it, I wouldn't go past the 1216cc 11:1 piston kit. Any more radical and you'll be having problems with HEAT.. and that becomes very real if you get stuck in traffic on a hot day... and no, i'm not talking about your COMFORT; rather the stress on the rings and bearings.
Again, it depends on what kind of riding you do.