Dan, I have a lot of problems similar to your own. I'm 38 now, but from age 17 to 25 I was a regular and heavy power lifter; at 17 I was 170lbs but at 25 I was 230 (6'3") with a 1400 lb bench/squat/dead total. I was hovering at around 8000 (up to 10000) calories a day - I am a very hard gainer. Right around that time, I started noticing that my joints were getting achy; I took a little time off my regimen, and the longer I waited, the more pain I noticed (endorphins/adrenaline was killing the pain). I got away from weight lifting as my joints got worse - right now, my joints allow me to do body weight exercises about once a week. I also have irritable bowel and a natural allergic reaction to corn.
A few years ago I started experimenting with Paleo (nothing processed, no grain, no dairy, no potatoes, no legumes - i.e. just meat, eggs, nuts, fruit, veggies), and am now on the autoimmune subset of that (no nightshade, no eggs, no nuts, no seeds, no NSAIDS, no alcohol, or cross reactive foods - Tylenol is ok for pain, but not so great for liver). I had found some definite improvements with my first incarnation of Paleo, but probably twice the improvement since getting on the autoimmune version. The main point I've been building up to is this: the pain in my joints is a sensitive barometer to what I eat - if I break down and have some ice cream (natural as can be) I feel like I have an awful hangover, and am achy for several days. One thing that I have noticed is especially important is the quality of the food I eat: fully grass fed red meat, free range organic chickens, organic vegetables - these things are as important to the way I feel as eating the right types of food. Eating a fatty grain fed steak gives me aches and pains; grass fed steak digests perfectly, and causes no flare up.
I also take a fair quantity of high quality fish oil every day (Carlson's with lemon and Green Pasture fermented cod), which seems to help joints a lot. Like someone else mentioned, I would be careful with the amount and type of fish you are consuming; heavy metal and parasite levels in fish are becoming insane (especially farm raised); at least get yourself checked for heavy metals periodically - no reason to trade one problem for another.
Right now, I'm at 170 again (exceedingly lean), though I eat to capacity at every meal - lot's of fat, lot's of meat. I have been on the autoimmune for about 4 months now, and am greatly hoping that some of the other folks are right about the healing of my gut leading to a general increase in health, and hopefully I will gain back a little weight. Thanks everyone for what you've written here. Dan, you're not alone in pain or difficulty in gaining. Let me know if you find any game changers.