In reply to Levy_danny:
Pain on the front of the knee underneath your kneecap to me is usually a sign of slightly too low saddle. Though I’d expect it in both. Pain in the back of 1 knee is typically a sign of saddle too high. (That said, it’s much easier to have your saddle too high than too low, so perhaps take this with a pinch of salt)
Generally the thinking in (ultra) cycling now is slam your cleats all the way back so you end up using less calf and Achilles. (You should do this for both feet unless you have a known leg length discrepancy) putting the cleats back can lose you a little bit of “snap” from your sprint, but for long distance cyclists hardly a problem.
In terms of aligning your cleats I recently watched a bike fitter do an interesting trick. Find a floor with tiles (so you have lines of reference), take your shoes off and close your eyes and walk on the spot then stop after say 10 paces. In theory that position is what you should be looking for from the cleats so angle them accordingly.
If you have mtb/2bolt cleats, there is another trick with alignment. Pedal on the turbo with the previous position, then stop with one foot (that you’re checking) at exactly 3 oclock. Then if you can get someone (or a camera) to check the front cleat is floating evenly on the pedal. Then repeat stopping the other foot at 3.
knee pain sucks, hope you can sort it out!