One thing to think about, you say that the majority of the pain is coming when you are going up hills or when you forget to shift down.

If you are pushing to big of a gear- knee pain is bound to happen!! So my advice would be to spin at a higher cadence in a smaller gear versus mashing a bigger gear, and see if that helps for a little while- even stay in the small chain ring for your whole ride.

Also fit and float like everyone else said!