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.
There are 2 other things that have not been mentioned, but should be considered in doing the big 3. You may want to mod your air box when you do K&N or UNI air filter. EHS lid is a good mod. You can get it either as a DIY kit or you can get it as an already moded lid you just swap with the stock air box lid.... 30 seconds or less.
When doing the exhaust upgrade, you need to be aware of decibel limits in your riding areas and if they have a USFS approved spark arrester. Many of the mufflers and full exhaust systems you can get can be designed for racing and may not meet sound and spark arrester requirements for trail riding. In California, we are limited to a max of 96db. It would be a bitch to select an exhaust system and spend the money only to find that you can't use it for the riding that you do. When you do your research to find an exhaust system (full or slip on)... look for the max db... If they don't say what the max db is, there is a good chance it's above the max allowed for trails. EXAMPLE, go to the site for FMF mufflers, you'll see plenty of choices of exhaust systems.... BUT, they only post the max db on one system... The Q4.
Somthing else to keep in mind about K&N's, they do provide more power, but at a cost...more flow means less filtration. I recently added a foam wrap to my K&N to provide better filtration after I sent an oil sample in for analysis and found unacceptable amounts of dirt in the oil causing high wear, I will see if the wrap works on my next sample...if not I will switch to a foam filter, to me it is just not worth the extra HP.