Although this is a result of injury, and isn't a medical condition, it may not be of direct benefit to the OP. But hopefully some others reading may get some benefit from this.
I have chronic pain in the forefoot of both of my feet. I injured them 3 years ago in a fall. I've had MRI/Bone Scan's/CT Scans/X Rays/Ultra Sounds. Seen physio's, GP's, sports surgeons, podiatrists, orthopaedic surgeons, chiro, massage therapists.
All scans etc. show there's nothing wrong but I still get pain. No doctors can tell me what's wrong. The best thing for me personally was the massage therapy. It helped a great deal, but after a while I no longer found it useful, as I could get just as much relief from massaging my own feet instead of paying someone else to do it.
I'm only just slowly trying to get back into it after more than a year off from all lifting and sports. I ignored the pain for a long time, still playing sports, then trying to take up lifting. I'd only been lifting a couple of months, but it made my pain get far worse. I ended up throwing in the towel, if I couldn't go 100% I decided to give it all up and try and rehab my feet and come back 100% fit. Running, jumping, walking, or even standing for more than a few minutes would make my feet even more sore for days. I took over a year off from regular sport or lifting, but still never fully recovered.
The best thing over that time was initially the deep tissue massage therapy. It hurt like crazy getting it done but it helped so much. I got less and less out of each session as I slowly improved. I also slowly learnt the techniques I got the best results from. So after a few months I could get the same benefits by doing the massage and stretches myself, which also saved me money.
Over the whole time I have been using heat packs, stretching, massaging and doing strengthening exercises. I've had to learn over time what I get the greatest benefits from, and learn what was overdoing it and making things worse. As my injury slowly improved (month by month) I'd have to relearn what stretches and exercises would benefit me the most. What gave me the greatest benefits 3 months ago, now no longer helps. Whereas other exercises now give me great benefits. Because my injury was already 2 years old once I stopped all sports and tried to rehab, progress was extremely slow. I never stopped sports originally because I saw countless medical professionals who all recommended I keep playing sports.
I don't believe my feet will ever be 100% again, but I've become far better at managing the pain, which I think is the key to chronic pain. Although I still aggravate the pain, I've learnt which exercises help the most. Now the extra pain may only last a day or 2, and be far less severe, whereas before it would be severe and aggravating it could last a week. I've begun dead lifting again and can manage to do that with no lingering pain the following day. I'll be starting squatting again shortly and see how I go. I hope to be able to return to basketball, my true passion, some time next year. I'm not sure if that will ever be possible, but I will continue to take it 1 slow step at a time.
I think the main thing with chronic pain is learning what triggers make it worse, and what make it better. Basically getting better at managing the pain. I don't think there's an easy answer here. It's taken me years to learn as much as I have about managing my pain, and really, I'm still no good at it. The second thing is probably to keep trying and to be diligent with any stretching and exercises. For me personally I often find it hard to find the motivation, as it's very easy to get depressed when you can't get out there and do all of the things you want to be doing. The other thing is that rarely have I seen any short term benefits from the stretching and other exercises. But when I look back, there has been a lot of long term gain by keeping at it, even though it's pretty much impossible to notice it at the time. So although it's easy to feel that it's not doing any good, keep working at it, it will help in the long term.
This has been my experiences dealing with my chronic pain. I hope my lengthy post can be of help to somebody out there!