Another thing to try in your search for pain free cycling is arch support. For years of cycling my right knee did not track straight when I pedaled. This of course put pressure on my knee. Finally I tried an arch support in my right shoe and it has fixed the issue. Apparently my arch would fall during the power phase pulling my knee inward toward the top tube. E-Soles makes some good arch supports if you want to give it a try.

What I leaned is that if there is pain keep trying things and don't give up. It may seem expensive but pain free riding is more valuable than anything made out of carbon or Ti.