Back in 1979, I had a bad accident that almost cost me use of my left knee. Prognosis was that there would be a full knee replacement in about 20 years. Since then, I have tried to led a normal life and build up the strength in that knee and it has worked. About August last year, I took up cycling and found this has been a great way to help an weak knee. However, one day my knees (both) were aching terribly and stairs became difficult for a few days. I rode the bike again and the same thing happened. It was disturbing and odd, but certainly connected to the bike.
To make a long story short, before you ride off into the sunset on your trusted bike, get a professional "bike fit" and use clip in shoes and pedals. Once that is done, ride conservatively and increase distance/time in the saddle as your strength and fitness improve. My guess is that you will find significant improvement and quality of life.
I wish you the best of luck and hope you post your results.

PS, I never did get that FKR and have no issues today. If it weren't for the scars, I would have forgotten about the injury.