You can order any of the 3 one at a time or all together. Ur local stealership can do this for u or u can shop online. Rockymountainatv.com is a great place to shop online. Then there's ebay and a hundred other places too.
For exhaust I think alba is the choice full system now for the xx. We've all been watching the r and d intensely here.
Imho, a uni foam filter is the way to go, although some others perfer the k an n. Its really a preference I think they're about the same, but again imho, the k and n is a little higher maintenance for the basically the same air flow.
The power commander 5 (V) is the way to go if ur gonna do all 3. It has an auto tune feature that's super cool. But the PC3 will do just fine, there r fuel maps all over this forum (I'd be happy to email u one) and I think scuzz posted em on here as a downloadable link. There are also some dobeck controllers (which r limited in fine tuning) like fmf, hmf, etc. However some on here have them and like them.
Bottom line, imho the best setup is...
UNI foam filter
PCV with auto tune
ALBA full ehaust system with auto tune bung... BUT
U can easily substitute the PC3 into this setup and be more than happy.
Get ready to open ur wallet tho.
There is also some very good engine kits available... Do some thread searches with keywords like pistons, stage 2 or 3 cams, u should get the threads for how to obtain an engine kit that way.
Happy hunting!