1) Definately call Jeff for your Top End! If you need your cylinders bored, he can handle all of the above at a very reasonable price, IMO, nobody does better work at an affordable rate. I've had cylinders done at many different shops local and elsewhere. I just got mine back from him and must say they are perfect in every way......
2) For the chain & Sprockets, check with Rocky Mountain ATV. I most often buy the JT or Sunstar sprockets. My preference is a steel front/aluminum rear....I like the 120 link chain and cut to fit. I'm running the TMDesign rear guide and front roller. No problems here. I believe Rocky Mountain has those also, you might check with James Lucky or Chaparral Motorsports.
3) For a standard wheel (No beadlock or reinforcing rings) I prefer the Douglas .160 or .190 for anything but sand. In the Dunes, the .125's work for me. I have a set of ITP Baja's on the rear of my Shee for dirt tires and like them alot (Even though they are kinda heavy). Again, Rocky Mountain has good prices, also check Hell Bound Racing or Recreation Tires.
Good Luck!