This post is a bit late. I did Squats on Monday before work. I am still having problems with knee pain. I have considered the symptoms and believe the problem to be an overly tight IT Band.
Here is a link to further explain things; http://www.speedandstrengthcoach.com/SolvingKneePain.html
I did some further stretching and although the knee pain was present at the beginning of the work out it gradually went away. That said, the thought of possible knee pain left my squats cautious and not as strong as I would have liked. It's tough to move big weights when you don't have confidence in your body.
Leg Swings and Stretching.
Squats - 135lbs/6 reps, 135lbs/6 reps, 225lbs/6 reps, 315lbs/3 reps.
Squats (with belt) - 3 sets/1 rep/405lbs, 2 sets/1 rep/415lbs.
Squats (with medium bands) - 3 sets/4 reps/405lbs minus medium bands).
Sit Ups - 3 sets/15 reps.
The sit ups are the first core work I've done in a while. The knee pain could be caused by several factors; weak core, tight or weak glutes, tight or weak hamstrings, or tight IT band. I will do my best to identify and rectify my problems.