I always found the problem with squatting is that i was trying to hold tension throughout my back. So when i reached parallel i couldn't hold onto the tension because i was forced to push my back forwards in order to develop a vertical line from where my heels were to where the bar sits, you'll know what i mean if you've read starting strength. I squat now with my knees going forward more, you can do this easier with olympic weightlifting shoes or putting some small weight plates (inch to half inch thick) under your heels when squatting.
I believe you can't squat olympic style or full squat unless your knees are going forward a fair amount. This style of squat means that you can keep your back upright instead of leaning forward to get the optimal position, you shouldn't need heavy weights to force you down into position like some people believe. I would ignore the idea that your knees should be close to vertical if you're trying to squat atg, this is only suitable for a powerlifting squat. Sorry i have no idea what your thigh problem is, this is something i had to get off my chest.