Read up, everything you want to know about these can be found in the 900 section.
Definately delete the radiator.
Ski's - I'd suggest Powder Pro's or Grippers.
Spindles - Stock set from a Raw or Holz, Zbroz is also getting high marks.
Airbox - Fire n Ice is supposed to be about the best, but someone posted a good "how to" on gutting and porting the stock air box. Stock box flows good the way it is, just makes for a crappy clutch cover and is bulky.
Motor mounts - update to the 06's or get the Compfusion kits.
Clutch needs balanced.
05 Pistons need updated to 06.
There is an update for the fuel tank.
Intake boots on the Throttle bodies are probably cracked.
There is an update for the chaincase cover, a plate to keep heat off the plastic cover.
Check you belt tension and side clearance, adjust accordingly.
Read up on different clutch setups to reduce heat.
Re-gear, again, read up on what people are using and what conditions apply to you.
Front track shock spring needs to be changed out to a heavier one.
That's kind of where I'm at with mine, after some great experience from people on this forum that have shared what they know about these. In stock form... they suck, but once "fixed" they can be a great sled.