The black-oxide bolts you are mentioning are a common Yamaha part. I had to pick some up last year to replace a few missing from my black trim inside the fairing. I think they were about 40-50 cents each.
As for the hex-head silver/chrome plated bolts, I have not had to replace any of those. You might try a West Marine location for stanless steel stuff (assuming you are near a major boating area), they might have it. From past experience, that sort of part in Stainless would be about $1-2 retail at West Marine.
