Just wanted to follow up on this thread and let you know what the outcome was. So I went and saw a physical therapist who evaluated me and also gave me a medical bike fit. She was a pro rider at one time, so I felt pretty confident in her abilities.

I had two visits with her. At the first one she looked at my body mechanics while standing and walking, and did some range of motion stuff to see how my joints were moving. There was no damage to my joints but there were a few issues: I always knew I had flat feet, but apparently I have one naturally flat foot and one fallen arch, so she made me aware of how that was making my knee turn in while walking and standing. It's something I can apparently compensate for without orthotics just by staying aware of it. I also bounce a lot when I walk, and don't fully extend my leg straight with each step. She told me to change how I walk to a straighter step so I don't stress the knees as much. And last she told me that the muscles on the outside of my legs dominated the inside, and that I could bring the inside muscles back into play by doing some glute exercises. I've been practicing everything she told me and my knees are feeling great, however I have not been riding at all so I can't say where the improvement has come from.

The second visit was the medical bike fit. Turns out I had my seat a bit too far forward and a little high, one of my SPD cleats was in the wrong spot and turned a little. I also ride with a rounded back, didn't lead with my heel on the downstroke, and was not keeping my thigh bone parallel to the top tube. So we corrected all the stuff we could and now it's a matter of me being very conscious of my riding technique.

I'll update this thread again in a couple of months and let you know how I'm doing. Thanks again for all the inputs.