I know EXACTLY what you mean...running into the same parts/pricing problems as you. My brother grabbed a handful of brake in a turn and basically flipped end over end. Bike was absolutely spotless before. Now, frame damaged, all plastic pieces on right side scuffed, brake lever, custom rear set, MIG exhaust canister, right handlebar are all damaged. Probably $4k to fully repair. There's a shop 50 miles from my house (G.M.D.?? in Jasper, GA) that specializes in repairing bike frames -- for $1200 they'll measure with laser and guarantee frame will be put back to spec (BETTER than new they say).
Also considering parting the bike out and using the money to offset the price of a newer bike (maybe a '07). Think I'll miss having/tweaking carbs and probably will run up a bill trying to get a newer bike to pull like my 1999. My brother has offered me $4k either way.
If you (or anyone else) have any opinion about which way I should go, please let me know. I just can't seem to decide...