Find a good physical therapist. There are some good ones out there, I promise. But you might need to travel and/or pay out of pocket. And the best source for good PT recs is friends in the same sport - so make friends with some ultra runners and ask them.

Hit the gym and do yoga. A big part of a lot of knee pain is instability in the low back and hips.

Read up on psychosomatic pain, and integrate exercises into PT and gym time.