Sonofsam,
I am not a doctor or health professional, so this may or may not apply to you. But there is a condition called lower cross syndrome which is caused by extensive sitting. This causes some muscles to become shortened while others get lengthened and weakened. Here is a link, but you can find tons of articles and videos about it.
Lower Cross Syndrome
As for squat depth, go as low as you can without pain while working on your mobility to go deeper. If you stop above parallel, a lot of the stress is handled by the knee joint and ligaments, which is not good. As you go below parallel, your glutes and hamstrings will kick in to help you on the way back up as well as stabilize the knee joint.
For squat mobility, check out the Youtube channel of a man named Kelly Starrett as a start. I actually found a solution a to a knee mobility problem that had been plaguing me for years, and multiple orthopedic doctors and physical therapists could not help me with. I cringe when I think about how much money I spent when all I needed was a $20 jumpstretch rubber band.