I didn’t see it mentioned yet, so I’ll bring up float. How much float do you have with your cleats? Couple years ago I tried out 0 degree float and had knee pain. Took me a couple weeks to figure out that was the cause. Then I went back to 6 degree float. It wasn’t an instant pain relief as my knee was still inflamed. It took another 1-2 weeks after the fix for the pain to subside and no knee issues for years.
Just this past weekend I bought fancy new shoes (S-Works Recon). First MTB ride with the new shoes felt ok, but a little tight and not super comfortable. I thought maybe the BOA’s were tightened too much. The next day I wore the shoes much looser, but 1.5 hours into z2 gravel ride I had intense pain below the knee cap (lateral, posterior). I haven’t had knee pain in years, and all of a sudden I do. The only change in my setup was my shoes and possibly cleat position going from one shoe to another. I moved my cleat up a bit (was slammed back as far as possible) to see if that helps. Will ride today and see if cleat position helps.