I do work in the health care field and have written close to one hundred health education and research papers, so I do have some background in this....but,,,,tough to tell without seeing it in person. Rather than trying to pinpoint your condition, I will give you some general thoughts.
-I would consider locating a good sports physician type in your town-could be a sports PT, MD or other, but these types of folks tend to look at our bodies more from a function and performance standpoint rather than a simple presence and absence of symptoms approach. That would be my starting point. I have always preached to guys that they need to locate a team of support professionals in their community LONG before they ever get injured or actually have need of one.
-I think if you train long enough and heavy enough, then it is going to have some sort of negative effect on the joints of the body-dont get me wrong, the positives FAR outweigh the negatives, but none of us are invincible and physical stress and micro-trauma catches up.
-The overhead squats have been wonderful-they have made my lifting not just better but more "fluid" if that makes any sense at all. I was making progress before I started doing them, but they seem to take off the rough edges and extra discomfort of the compound movements. A couple of years ago, I was having a lot of little "twinges" in my knee, nothing real severe, but after a game of basketball with my teenage son and his friends, they would ache and be stiff the next day. I started doing a lot of free hand bodyweight squats for high reps and even some hindu squats and after about 6 weeks of doing that, I noticed major improvement and have not had any problem since then.
-look to the mineral/supplement chest, I think taking some type of joint formula with glucosmine is a great idea, I also take magnesium, zinc and some other minerals.
-consider some type of custom fitted orthotics for your shoes-what is the wear pattern of the soles of your shoes like?
Just a few thoughts-maybe Dan or others can add to this