As mentioned before, I'd get a hold of whatever polishing cloth your local machine shop uses on their cranks. Then, continue your efforts.
The discoloration is hard to determine. That could be as major as the hardness being worn through or simple as temperature discoloration. It'd be great, if you could get an engine machinist under there to take a look. Offer him a premium 6-pack, or whatever, for his time.
I think you're on the right track of bearings, oil pump, and minimal other parts, though.
'09 Triumph Tiger1050
'96 Ducati 900SS
'02 Suzuki SV650S (hers)