If the MRI's are negative it has to be biomechanical and maybe fit. All the clicking in the knee is because the knee is tracking wrong due to some kind of response to over-use. You got some muscles over-developed, some tendons under-developed, a lot of tightness and it's causing the kneecap to be pulled out of position. I'm guessing all this cos I have the same issue. Had to stop cycling last year because of it and was hobbling for a few months the knee was so bad. Rest and lots of stretching from the hips down and strengthening of the muscles around the knee is all that's helped me. When you get back on the bike limit distance and stay away from hills. Build up slowly and always rest the day after a ride.