Hey,
I'm with you. I've just recently purchased a '00 650R. There are 4 layers to the backfire screen, I pulled out 3 of them and crimped the frame back together. Very easy, clean and works great. I know XR's Only sells a less restrictive screen, but I can't imagine it being any better than a modified stock one.
I've heard about raising the needle (richer) to the 4th position, down from the stock 2nd position. I did that this morning and I'm pleased with the results. I think I still need to richen up my pilot jet though, soon I hope.
Also, the crankcase breather tube (going up to the airbox) gets smashed between the seat and the frame which can cause blown countershaft seals. I rerouted mine under the frame, up by the shock canister then to the airbox. I think the newer 650R's come with a new part number for the c-shaft seal, so whether it is the seal or the breather tube's fault it's hard to say. Probably a combination of both I would guess.
Finally, you didn't mention it, but did you remove the plastic plate and snorkel in the airbox? Good luck, and enjoy the beast!