After about a month of on and off development I am proud to say that
After chatting with the chiropractor on Friday I learned my pelvis is shifted forward to the right. Which was causing the right leg knee pain I have been getting. If I shift the left pelvis/hip forward the pain actually goes away. I am working on different riding positions to see what causes pain and what relieves it. I am amazed the way the body reacts in motion.
There is a ligament [Posterior Cruciate Ligament] in the rear of the knee that if it is not working correctly forces some uncomfortable pain in the knee after lots of riding. The pelvis being out of whack pulls my leg wrong and after a while I get pain. I thought it was my pedals, which technically it could be since I am locked in via clipless pedals.
This is why you go see the people that study this stuff. Bodies are like systems, you just have to go to the right tech to fix them. Hopefully through exercise and some treatment we can get things under control and spinning correctly.