YW bones.
I have to add, that because of HMS I never can run pain free anymore, but the bonus is since I've started running regularly my knees and ankles are stronger and more stable. I used to wreck them every month (just normal walking or going up or down the stairs), but now I hardly twist or sprain them anymore. Wobble boards are fantastic tool to improve your proprioception and stability. There's lots of exercises you can do to make it more beneficial (and fun!). I do controlled squats, using both legs and one leg at a time. Dont feel discouraged if you can never make it work the first time - after a few days or weeks it'll be second nature and you'd do it without conscious thought.
You have to know and respect your body limits, I try not to take any painkillers right before my run, if need be take some paracetamol maybe 2 hours before. Not less than that as otherwise you'll just mask any potential injuries you might do to yourself in the run. Even being a regular runner, HMS does make you a bit "clumsy" every so often in my training sometimes I feel like I "lose" my balance, or land awkwardly on my feet (threatening to twist it!!!!). Thats why i'd recommend you WALK the first few weeks first, lots of wobble boardings. Then you can try to run.
Remember - your Cardiovascular system improves much MUCH faster than your ligaments and joints adapt to the impact. Just because you dont feel "out of breath" does not mean you should run more! Take it easy! I did a mistake of increasing my mileage too quickly ( CV-wise I'm quite fit as i cycle and row a lot) and put myself out of action for 3 months because of torn ligaments in my knee.
The serpentine running club has lots of good tips. Remember to double or triple the "introductory phase" mentioned due to our bendy nature and you should be OK.
http://www.serpentine.org.uk/pages/advi ... nners.html" onclick="window.open(this.href);return false;
Warm up sufficiently. Cold muscles and joints tend to injure easily. Stretch a bit (not too much, as we're stretchy already) within normal range of motions. Cool down after your walk/run and stretch again to help reduce soreness.
http://www.runtheplanet.com/trainingracing/stretching/" onclick="window.open(this.href);return false;
Have fun

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Edit to add:
Runners (even non hypermobile ones) can get lots of pains and sprains. DONT OVER DO IT! You're running to enjoy it, not to wreck yourselves!
I hv recurring plantar fascitis, ITB, snapping hip, achilles tendonytis, scarred ankle (from a really bad dislocation) to name a few. Even dislocated one of my big toes runnning once! However, with a lot of patience and being more in tune with what you can do, you can actually run and enjoy it. Ice sore areas. Ice & Ibuprofen gels helps with soreness. massage oil containing cinnamon oil or capsaicin helps with aches.
If you have bunions, stuff cotton wool between your big toe and it's neighbour. Gradually stretch your foot (heel raise and lowering with your toes on the edge of the stair) if you have plantar fascities. Achilles tendonytis benefits from contrast baths.
If like me your skin chafes and peels easily from rubbing with clothing/socks, get body glide (its kinda lubricant marathon runners use on sensitive areas LOL. Not the adult lube *wink wink*). Wear PROPER FITTING RUNNING shoes, not just any trainers - makes a world of difference.
Just like any drug, running IS addictive. Pace yourself. Cant emphasis it enough. I reached the point where I wish I can go running everyday, but my joints (and my doctors LOL) wont let me.