Update on my transmission.
Took the trans. up to Anton at Va. Motorrad in Charlotesville for inspection/repair. Once inside it was found that the Input shaft gear had pounded itself into the bearing and broke the bearing seal releasing the bearing lube into the the gear box. That' what caused the discoloration.
And it turns out that this is a good thing. Had the lube not been discolored I wouldn't have known I had a problem as the transmission wasn't showing any other symptoms.
The gear isn't cheap at $240. With bearing and seals and 4 hours labor the bill came to a tad over $600. Less than I expected.
Anton has a small, cluttered shop on the back of his house. He's hoping to expand soon, but with the economy as it is he's waiting to see how things go.
That aside, after watching him work I was very impressed with the attention to detail. The shimming of these trans. is an art unto itself. I will be taking more work to him if needed.
I've enclosed a picture to show what went bad.