A little background before we get started:
I'm 22 years old. I got into nutrition and training around 3-4 years ago. I was born with a condition known as clubbed foot(I have it in both, it was severe). Long story short, by the age of 5 I had three surgeries. And started walking later than most kids. (I think I started around age 2? Not sure). Anyways, fast forward to high school. I wasn't active. I was overweight and unhappy. My feet ached and my body felt wrong. So I lost some weight. Ended up at 20 years old having another surgery, and another just last year. Totaling 4 each foot and 1 procedure each(injecting the joints to "fix" the pain).
Well, due to the nature of the human body. Everything has been effected. My knees track inward(knock knees) and my hips are in misalignment. Thus putting strain on the middle of my back.
This leaves me with some problems. I cannot properly train my legs. Nor be very physical, without paying the price. My knees ache when I squat, and cannot even reach parallel at times. Lunges the same, God forbid I do any leg machine without my knee(s) popping out of place above 50lbs. When I squat. My right hip, feels like it is just aching. Like something is out of place, a dull stabbing pain. Don't even get me started on ankle and calf tightness.
I need to correct my knees. My hips, the tightness I feel in them. Before I end up an overweight, wheelchair bound, old man in my future.

It seems no matter what I do, nothing helps. I'm in desperate need here. And I know I'm new, but I am trying to post more. I would love someday, to lose what Weight I have and bulk up with a cycle or two. But, with my body in the shape it is, it would be a waste.

If anyone could shed some light, It would be greatly appreciated.