Fixed it
Thanks for the extensive info, this makes it much easier.
I haven't read "pain free", I only have the Egoscue Method. Appearantly pain free is from 1998, new edition. I don't think there's much difference with his first version however.
You're seriously misaligned

This is going to take some time Rob. Took a few years to get into this situations, will take a few months to get it fixed. Persistence will be key, that and correct technique on the egoscue exercises.
First comment. I assume the exercises from egoscue method are in pain free too.
- Continue shoulder dislocations pre workout. Post workout: the arm circles & gravity drops with scapular retractions. The gravity drops are probably the best one to make the hip/shoulder connection. One hip is higher because of tight leg muscles. You can see the link with your shoulders. Gravity drops work both. They're hard but in my opinion one of the best from the book.
- Hips. Downward dogs will take care of hamstrings & calves, they'll probably hurt as hell, continue doing them until they do'nt hurt anymore. Gravity drops will also take care of calves. Runner stretch is also good for the hams. The downward dogs will fix the lower back rounding at the bottom of the squat.
Might also be a good idea to learn how to stretch to relax muscles. Pavel Tsatsouline's book "relax into stretching" is a good one. Stretching scientifcally is also a good one. I always stretch like this: tightening the opposite muscle as hard as i can for a few seconds (like 3) then lose the tension. If you check this video, you can see me doing it: I tighten my glute, release the tension and you can see a drop, this is the stretch you want to go after. You hold the stretch for a few seconds, switch legs. Repeat.
Video, check the drop at 35 seconds