OK - so my chiropractor told me that I have overuse tendonitis in my knees. That's good news actually because I know what to do for that. The knees are getting better - just the left one has some remnants of an issue. I think the other problem and what probably led to the tendonitis is lack of strength. As a result, I'm going to emphasize building strength in my legs in my workouts. So going forward in the near future, I'm going to do one or two interval workouts per week, a tempo (10k) run, and a long run, preferably a 16 mile run on the track. I have a few other things in mind for building strength which I've done in the past: Riding the bike, running very short sprints up the side of levees, and dragging a tire. No lifting weights yet but that could be in the future.
The other thing was that I went to Roadrunner Sports and had them do the gait analysis. The main thing we noticed was my left ankle rolling lightly which they said indicated my arch was stretching too much. So I got the advised arch supports (which I just ran in) but also will try some arch strengthening exercises.