The key for me has been strengthening exercises which are targetted in the middle of the range of movement - ie the 'normal' part of the range.
So - I have no problem hyperextending my knees to - 20deg. I also have very lax cruciate ligaments (effectively non-functional). So I target leg strengthening exercises where my knee only travels between 60 and 90 degrees of flexion. This might be squats where only go up and down a few inches. I also do a lot of cycling, where the range of movement of hip, knee and ankle are all very modest and so on. I think the reason this helps is that it increases the tone of the muscles which cross the relevant joint, providing a bit of external bracing. I know my knees will still pop all over the place if I consciously relax, but during normal running they feel much more stable. Still a bit iffy if I overextend while fellrunning downhill, but I just avoid this.
I'm not sure how you would extend this principle to ankle exercises, which need to provide stability in more planes and directions than the hinged knee joint, but I do know that cycling a lot has helped my ball-and-socket hips over the last few years - I feel much more 'solid' now in my 40s than I did in my 20s.
As you might imagine, I am hypermobile as well. I'm also a GP FWIW.
To the OP - I get your frustration. You're right to say that your hypermobility itself shouldn't really cause much pain - but it leaves you prone to injuries that can. If you had such an injury, though, it ought to show up somehow. They're elusive buggers though, so it's perfectly possible that there's nothing to see on XR, MR etc. 2 years continous is unusual, mind.
I'd also agree that fibromyalgia is a syndrome defined by widespread pain - you can't really attribute continuous back pain to it.
Don't despair - there are a few threads on this site involving people who have managed to maintain their running. Personally I have to cap my weekly mileage to about 35 mpw or my knees swell, I also have to change shoes pretty regularly - about every 250-300miles - or the small joints in my feet swell up. I tend to rotate swimming and cycling as well (the latter has really helped my knees- plenty of hill climbs) and have kept my tendency to flare up to a minimum. I've now got 4 ironmans and a few marathons under my belt, so despite the niggles, I still get out to enjoy myself plenty.
One final thought - no all back pain is musculoskeletal - has anyone considered eg endometriois as a cause of both pelvic and back pain?
JS - shall do. She's just tucking into tea. She might be a while!
Some staggering efforts and times there - you can only have managed that on the back of some very committed training. From the sound of things on the event's thread, some folks hadn't prepared as well- it sounds like carnage at the end.
Well done to all who survived today. They must be just about the hardest running conditions possible. Glad I wasn't manning the medical tent at this one.
Dead proud of Mrs BTB, though - 2.06/2.05 splits for a big PB. Well 'ard.
Now her main event's out of the way I'll hopefully get some time to get out for some long runs with you all. I've a bunch of 20+ milers which don't involve either Morrisons or the MWW if that would tempt anyone.