Sorry to hear about your joints hurting. I know it just plain sucks. Every once in a while my knee goes and gives me trouble. (old nursing home injury)
My dad's a pharmacist, and when he was growing up on the farm his arm would pop out of joint all the time. Years later he had that fixed, and then again fairly recently got that fixed again, this time removing bone spurs and doing a total shoulder replacement. He's used naprosyn, and that helps him a little (drink tons of water!!).
Glucosamine Chondriton may help you. I think what it does is add to the joint tissues, providing more of a cushion and padding for wear and tear. (not too sure though) I'm going to be trying it too. I'm tired of the knee aches! Also it might help my shoulder a little. My sensei tore out his shoulder a few years back and he was put on some steroids and had a lot of therapy. I think that they also put him on Glucosamine, not sure though. But he's fine and happy.
You mentioned that you wanted to lose a little weight. My advice there is to change your diet. (Diets don't work because after you get to the desired weight you go back to your old habits.) You mentioned that you had been eating one time a day? Get your metabolism working for you. I've seen that if I eat several mini-meals during the day my metabolism goes up.
I've tried chiropracters and my reccomendation would be to find one who can manipulate your spine instead of forcing it. I've found one that I'm impressed with and I'll stick with him. I was a little cautious about acupuncture, until pain in my lower back forced me to find something. I really enjoyed it, and it helped me out a ton!
If the rough and tumble of Aikido is not helping you, then you might try some alternatives that are just as fun and have some of the same principles. I tried Tai-Chi a while back (didn't last because I wanted to do something more active, but I really enjoyed it) and some of our older students do it also. It doesn't have the high impact that Aikido sometimes does, and it is great for developing stamina and strength. (I love Aikido, so I would hope you stick with it.)
But it sounds like you are the right track by seeing multiple doctors and the fact that you are looking for a cure. Best of karma in finding it!
BTW, you mentioned that you live near a processing plant. Do other people around you seem to be having the same type of problems? (esp your age)