I hope you figure out the issue and solve it so you can enjoy riding again.

I've had similar issue with my left knee(behind the cap) pain. It happened after i changed some parts on the bike and although i thought my position(fit) on the bike was optimal, my knee was telling me otherwise. I fiddled with everything, adjusted pretty much all the parts that were adjustable, and finally when i stopped using clip-less systems, the pain decreased. Its not completely gone, but at least i don't feel like my knee is rusted and can keep riding all day. I am going to get a professional bike fit this winter to prevent any future problems since I plan on riding 600K with the Randonneurs next year.

Some things to consider:
Age- the older we get, the longer it takes to heal, and some parts take a lot longer to heal than others.
After its all healed, you want to do the same thing you were doing before the problem, but you body is not at the same fitness level and you have to build back up. Be very patient and do not re-injure yourself. I've done this before thinking all is well, but then not so much.
Do you spin on the bike when you ride or do you mash it? I like to mash, but if i want to keep riding in my 60's, i better keep spinning, more so when riding loaded or climbing.
Another difference might be getting a 44/32/22 crank with 12-34 or even 12-36 to help those knees.

This is so far from my experience. Others might be more helpful. Whatever it is, don't give up. Life gives you lemons, make lemonade and share it with someone. I have learned a lot from this forum and still have a ton to absorb.

Good luck