I had never heard of this, so was curious as I suffer a lot of pain in a lot of areas and have had enough physical therapy that it almost completely fills my awake hours. One interesting point made on one website was not to do range of motion exercises if you have this, and should in fact reduce range of motion in your exercise. There doesn't seem to be any reason to limit most exercise as it's going to hurt anyway, which was also odd advice (from a runner's magazine). Painkillers I'm not so sure about unless absolutely necessary to function, as they mask pain but don't actually do anything about it and can therefore allow injured people to do things that injure them more. It can be important if you make your living doing physical exercise, such as a pro athlete, but for the average person you want to know when a movement hurts so you can alter how you do it or avoid doing it. The cracking and popping is interesting, as that is more often associated with torn cartilage. It is possible you have more than one problem, but I'm guessing you've had MRIs and seen orthopedic surgeons who have manipulated your knee given that's how they apparently diagnose this condition, which is also oddly associated with an oversized amygdyla, which is what governs the flight or fight syndrome of panic attack sufferers and is associated with elevated cortisol. All very odd stuff. As your doc instructed you to in fact limit range of motion, which is an obsession with physical therapists, it sounds like he has a good idea of this condition. If the cracking and popping isn't associated with cartilage problems and doesn't hurt, maybe it's benign and you just have to get used to it, but I'd ask your doc about this because, again, this is often a sign you might have, say, a torn meniscus. You can, of course, have two different problems at the same time. A really good way to work your quads with very controlled motion is at the gym with a seated leg lift machine. I wish I could tell you what to do, but everything I saw says it's okay to exercise, but you do have to control that range of motion to minimize the pain. But as it's suspected to be a genetic problem, you'll have to learn what you can do and what you can't but I don't see that it can be cured but as mentioned above, it's often seen in young people and often gets a lot better over time.
Here's from another website:
"Joint hypermobility syndrome often improves as you get older. The main treatment is improving muscle strength and fitness so your joints are better protected. Your doctor might refer you to a physiotherapist, occupational therapist or podiatrist for advice. These physical therapies can help to: reduce pain and the risk of dislocations, improve muscle strength and fitness, and improve your posture and balance
"Treating joint pain --
"Paracetamol and anti-inflammatory painkillers (like ibuprofen, which comes as tablets, gels and sprays) may help to ease pain."
It sounds like you are on the right track, and that with this condition, time itself can be a healer also. If you feel you've been given the wrong exercises or advice that hasn't helped, tell your regular doctor and ask for a referral to someone else. I would also consider yoga, tai chi, swimming, or some of the other forms of exercise that aren't high impact. Try not to despair, there are a lot of ways to strengthen your muscles and improve your posture.