The cranks are heat treated, that explains the odd coloring. Hey, there are machine shops that do metal spray build-up of crank journals. It's actually not horribly expensive, maybe $180 to build-up and grind an entire v-8 crankshaft. I've never heard of anybody doing it for a bike, but it should be feasable. Make sure the crank is true before they do it.
Dirt bikes can be a real pain sometimes. My friend went through something similar. We were just going to put a new piston in it, the bike ran fine other than a bad left side crank seal. Next thing we know, we're putting a new cylinder on, the bike needs a new clutch basket, and as everything finally goes together, he accidentally torqued one of the head bolts to the cylinder base bolt specifications and busted the stud. Every bolt on the bike was seized up, making things really difficult. The linkage bearings were out, the swingarm pivot bolt is stuck in the engine. The bike is only 5 years old and he just bought it. He was very frustrated, but everything was worth it when that bike started up again.
Hey, when you put everything together, be sure to use a torch. It makes bearings go from can't be driven in with a plastic mallet to drops in with gravity. I just put my cases back together today.