I have osteoarthritis on my fingers and left elbow from over use. Sometimes this areas are painful.
My knees don't bother me even after long riders (>200k). They get a little stiff, but that's all. My cadence is around 65 rpm on hills unless it is very steep, and then it drops to 55.
Is the popping continuous? Seated also?
Do yr knees bother you after a ride?