Hi Margo,
Whew! From the sounds of it your quadratus lumborum is contracted, and that usually means that the erector spinae and gluteus maximus muscles are also in spasm. Since you've been to all the doctors and had all the tests, we can be pretty sure that muscles are the problem, it's just a matter of working out the source of the pain.
I wish you were here in Texas (or North Carolina since I'm teaching two workshops there) or in New York (I'm working in Piermont on April 29th). It's a real challenge to figure this out via the forum. Do you know a good massage therapist in your area, someone who is trained at trigger point therapy?
I'm glad to see you aren't stretching your hamstrings, I think it's best to leave them alone until we can find the cause of your pain. You could do some of the treatments with the ball, but be gentle and don't stretch. Since your erector spinae and QL feel sore and swollen, I think you're right that it's because they are tight, and since you get some relief when you do the full protocol, that's probably the reason.
Did you get Sombra when you were at my shopping cart? Sombra is really good at going way deep into the muscles and helping them to release tension. I use it here when I'm working on someone with chronic muscle tension. Also, arnica gel is great for after treating yourself because it heals bruised muscles and lessens swelling and pain. My athlete clients LOVE it. One other thing that works well is soaking in a hot tub of water with two cups of Epsom salts, it helps to draw toxins out of your body. In fact, if you have access to a real hot tub with jets, that is another way to get the muscles to relax.
Look at a professional drawing of the iliopsoas and see exactly where it inserts into your thigh bone. There is one spot at the very top of your leg where you can reach this muscle and treat it very effectively. It's tricky but with determination you'll find it. When you do, hold the pressure on it for 60 seconds and then continue holding the pressure while you try to lean back (stretching the muscle).
As for your thumb and hand, the numbness and pain can be coming all the way from your neck (scalenes), pectoralis minor (impinging on the brachial plexus and therefore the three nerves to your wrist and hand), the biceps, flexors, extensors, and a muscle of your thumb called the opponens pollicis. If you go to
http://www.carpaltunneltreatment.org you can read all about it. Since you play the flute, the odds are your sternocleidomastoid (SCM for short) is involved in this situation, and also the way you sleep can be a part of the problem if your head is turned while you're sleeping.
I think if you just continue searching, treating, and having the patience that you obviously have, you'll find the answer.
Wishing you well,
Julie