It's very common that you will find pain in one knee and not the other. I suffered from right knee pain that was a combination of saddle height and also some more pronation in one foot compared to the other. Wedges in one shoe fixed that. Some people do have different leg lengths that can cause this, as well as muscle imbalance.
I'd consider raising your saddle back a little, and see if that fixes your situation. Sit bone pain could also be caused by saddle tilt or frankly you might just not have the "right" saddle for your backside yet.
Good luck.