The shop says it has a noise in the bottom end so they are assuming since the rod and cylinder are scored so badly, the crank is too. It ran low on oil due to it burning so much before anyone noticed. Shop says the head looks good but if that much dirt was in side the engine and it was low on oil, think I'm gonna just do the re-man'ed motor and start over.
Correct on the plating of the cylinder. Sometimes it can be bored and re-plated but no one (even Yamaha) makes oversized pistons. From what I've found, you can replace the sleeve in the cylinder but it is very difficult and the expense would be close to just buying a new cylinder.
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I've earned the names "Treefan" and "Deerfan"...