Basically started with the low bar squat (following StrongLift 5*5) but being very skinny (179 cm, 58 KG) the bar doesn't rest at the shelf created in scapula as described by Mark Rippetoe in this video. If I try going that low, the bone hurts there. This led me to squat with the bar a little up, somewhere on the traps, which qualifies for the high bar squat. Things went smoothly till now, when for the last couple of workouts I noticed a mild knee pain afterwards, its just some sensation that I know goes away with rest.
Secondly as the weight has got a bit heavier the current bar placement also feels on the bone, which I guess causes the thumb to go numb after the workout. Here is the video I shot today to check my form.
Please advice me for these two issues and point out things that I can do to improve my squats and bear more weight.