Damn I havent been on this site for awhile because of work! Looks like the questions havent changed much though, my usual answer would be NOSS as always......
First off- welcome to the forums. Second- Try doing a search and posting in the right forum. Third to get to your question- it all depends on what kind of riding you will be doing. There are a lot of great pipes out there, it just depends on what you are looking for.
Some people cut thier airbox and leave on the back part where the bottle sits. I was too lazy to do that though, I just bought a bottle relocator for like 15.00
I run the 22x11x8 8 paddle Skat Trak. I wouldnt trade the 22's for 20's for anything. I dropped down to a 13 front tooth. It rips up the hill at sand mnt. I preffer the 8 inch rim over the 10 inch. The 10 inch imo is a rougher ride over whoops. I have also heard its easier to spin the rim inside of the tire on the 10' rim over the 8's.
I just started using Amsoil's coolant. Its the exact same ingrediants as engine ice- propelyne gycol. And for 20.00 for 1 gal of concentrate that needs to be mixed with water is a pretty damn good deal. You get almost triple as much for about $3.00 more than the engine ice. I'm sold on it.
I almost bought a set of the Trinity pipes but I decided to go with Cpi's. I know Rnbrad is running the Trinity Pipes and has nothing but good to say about them.
Reeds, lighten flywheel, advance timing, noss head or mill the stock head. Then if you want to really beat thier asses port it and put on some bigger carbs.