My hips are wrecking my life

Hey body mechanics. I have a very chronic problem that I have yet to find an answer to. I have had these issues for the past couple years and it is driving me crazy. I am hoping someone here can help me.

Background- Firefighter, very active, lots of weight training and other metabolic conditioning workouts.

History- Ruptured my left achilles in 2010. I tweaked my left SI joint several years ago. It came and went but a couple years ago, I really messed it up to where I couldn't bend over without lots of pain. Went to a cranial-sacral guy and he was magic. My right leg was short and after the first session it was normal. Kept on working out the same and eventually his treatments stopped having a huge effect. Obviously I needed to rest but you can probably guess why I can't. So now my left SI joint doesn't give me too much grief if any at all. Now I have a whole new set of problems.

1- RIGHT chronic achilles tendonopathy. Started when running over a year ago. Came and went twice. I feel like I am a constant over supinator on the RIGHT side. Left feels fine when I run. Running and long walks hurt my RIGHT achilles. Painful to rub or massage. Dorsiflexion on both ankles basically equal. I do ALOT of soft tissue work on the right and left.
2- When squatting, from the front my left side thigh is several inches higher than my right side. Right seems to come forward more and the left seems to flare out and externally rotate more. At the bottom of the squat, my midline seems to be more shifted to the left side than centered. I can level out my thighs if I place my right foot forward several inches and then squat.
3- RIGHT sided hip pain comes and goes. Sometimes it is so sharp that I almost crumple over on that side. It is not constant but happens after squatting or running.
4- RIGHT knee pain symptoms come and go with hip pain. Coincides with right sided quad pain. Always after squatting and running.
Any ideas for you geniuses out there? I really wanna be able to run again pain free and squat without twisting and being uneven. Any help is much appreciated. Thanks!!