You are spot on. I have some knee pain in both knees with my new position. I had no problems with knees before. After locking at some youtube i suspect that i have my saddle to low now. At 12 a clock my bend in the legs is to much, more than before from what i can see when recording myself.
This is the video i looked at, he seems to know what he´s talking about. Bike Fit | Causes of Knee Pain and Solutions - YouTube