Not to make this a chorus but the advice to see a doc is spot on. If you're on a 2 or even 4 week trip and somethings hurts and you decide to bull through it, that's one thing. You're on a 10,000 mile trip, that's completely different. That's a bad sign that you were off the bike for 6 weeks working and the first day back riding your knee was hurting.
The other point I'll make is just how subtle these things can be. I was having some small amount of foot pain shortly before I left for my trip in September (also in the Sierras). I went to a podiatrist and he thought it was too close to my leaving to do anything permanent to my insoles so he put a little piece of adhesive foam, maybe an 1/8" thick under my insole where he thought it would help. I went riding and it felt good. A week into my ride my knee started hurting in a way it had never hurt before. The only thing I knew that was different was that 1/8" thick foam. Pulled it out and the pain went away within a couple of hours. If you make a change to your position, ride with it for a little bit unless the pain is getting specifically worse. Be very cognisant of changes that made things slightly better (or worse) and slowly dial it in.
I'm sure this is very frustrating for you. Good luck getting it right.