OE bearings are going to be KOYO or NTN. You can find them by size/type if you know the right supplier, but that's pretty tricky. On the other hand, it looks like they're still available through Polaris. For the rod bearing, some piston kits come with a bearing, and you should be ok with that. It may not be OE quality though. If it doesn't come with, I'd buy it from Polaris. They're $20/ea, where the cheap ones are around $10 – not a place I'd try to save $20. The crank bearings are a more complicated story. It would be a good idea to check the runout before you do anything else; I've got an 800 sitting around that was running when it was pulled, but the runout measured at .015 (FSM says no more than .004), so assuming it's ok is a big roll of the dice. If it's out of spec, then you'll want to send it to someone to replace all the bearings and put it back to true. If it checks out but one or more of the outer bearings feels rough or has excessive play, then you could replace the questionable bearing(s) if you have the appropriate pullers (or take it to a machine shop). The 800s tended to have crank problems, and you'll want to at least make sure you're starting off from a healthy starting point, especially if you want to build more power.
There were a few companies that made single and twin pipes for these, and I think SLP may still have one or both still available. I'd give them a call if you're looking for something new. Pipes off an '03 SKS should fit, although I'm not 100% sure of the interchange – the safest bet is to get the part numbers and call the manufacturer. Make sure you get all the pieces if you buy used; the pipes alone are useless. Most reports are that twin pipes give you the biggest power boost if you can tune them right, but tend to make the engine a lot more sensitive to elevation, temperature, and such. There's plenty of discussion if you search through old threads here, so I'd look through that before you commit to one or the other. It also wouldn't hurt to wait until you've got the engine up and running right before you move away from stock.