He was new to squatting correctly. He had done half squats in a Smythe machine for years.
I know you can squat I just don't know if you are squatting correctly.
What helped my friend (and may help you) was:
Reading Starting Strength and the FAQ page I linked.
Starting over with the bar only on the 3x5 program.
Making sure he could squat all the way down below parallel with feet shoulder width or a little more, toes out, knees way out over toes, feet flat, ass back, hip drive, low bar, straight wrists, chest up, etc...
Staying with the bar only for several workouts until he could do it right.
And having somebody stand there and tell him what he was doing wrong.
How do you make the decision between the 3x5 and the 5x5? Here's how:
If you can progress every 38 hours by adding weight (even a pound/kilo) to your squat every workout then you will get better results with the 3x5.
Since you are starting over with the bar and an instruction book, you can progress every workout on the 3x5. Just reset your other lifts minus ten percent (according to Practical Programming, Rip's second book.)
The 5x5 is designed for trainees who can no longer progress every 48hrs. Since you are starting over with squats that does not apply to you.