Suggestions for Cycling and Knee Pain?

** First, and completely off topic for the post, I want to say that you all are some amazing people. My most sincere thanks to those of you who went to vote (and passed along the link to others) in the Pedal the Plains "Plain Pedaler" contest. I try not to ask much of others via social media -or the blog- but this was something I really would like to do, and I am so grateful that folks (many of whom have never heard of me, spoken to me, read here, etc) took the time to go and vote. There is no word as of yet in regard to the outcome of things, but regardless of what happens, I just wanted to say thank you.  :O)  **

As some are already aware, one of my knees is not the best. I had an injury in my early adult years that caused some water on the knee and other issues and since that time, that knee has never been quite right. As long as I don't do anything too terribly stupid, I seem to be able to manage things. Other than long flights or events in stadium seating, I seem to do okay, and even then, as long as I get up and stretch occasionally, pain is minimal. Once in awhile, I have some issues on the bicycle, but those are generally when I've been pushing too hard (either with climbing or distance - or both) and it subsides over time.

Over the last year (or so), I have started experiencing pain in my "good" knee, however, and I don't know quite why nor how to resolve the problem and I'm hoping someone may have some suggestions or ideas as to what is taking place.

*Image from Runner's World

Initially, I thought the problems were due to improper set up on the bike, but after many adjustments, fittings, etc, that doesn't seem to be the problem. I also do a decent number of knee-strengthening exercises throughout any given week and have for some time now. While it's possible that the exercises could be causing some of the problems, I would hope that something meant to strengthen the knee isn't actually doing it more harm (and I try to pay attention to the things that are perhaps less beneficial or are flat out painful).

Generally the thing that seems to set off the knee pain appears to be time. At a certain point in a ride, the knee simply starts to ache or sometimes has shooting pains through it. I have tried to make some associations with the way I mount or start riding the bicycle when stopped as this seems to trigger it late in the ride, but I'm still not convinced that is the problem either. I have noticed that when I push off with the bad side, I do seem to trigger something in the good knee though - and I still haven't quite put a finger on why or how I am doing this, as the majority of my body weight is concentrated more on the bad knee.

The exact location of the aching/pain is pretty well centered in the area of the green circle on the diagram above (so, on the inner portion of the knee, and sometimes the right side- just below the knee cap). I don't think the pain is anything that will prevent me from continuing to cycle (particularly as I have cycled through it for the last year), but it would be nice to find a remedy to what has become an ever-increasing problem.

Do you have suggestions as to what this could be, or have you tried an exercise that has helped you alleviate knee pain when cycling? I always believed cycling would be less stressful for knees (at least compared to running), but I seem to still experience pains and would be interested to know if anyone else has found solutions.