Few things for you to think about:

1. After knee surgery, the stationary bike is like the first thing you do in therapy.

2. Mashing high gears is not good for your knees at all, but spinning faster IS good. Since you said this happens when climbing, try to switch to an easier gear and spin faster while climbing instead of staying in the same gear and pushing really hard.

3. Do you get this same pain when walking up or down stairs?

4. Next time you ride, put regular pedals and regular shoes on. That way, you can experiment with your foot position to see exactly where the problem is coming from. (If you have to change cleat position just to experiment with another foot position, you won't experiment very much).