I agree with what Dujin says. You can see that you are not getting depth-- "knees out!" is a good fix for that.
It is hard to tell from the video but it seems like you're trunk is loose. If you look at the fourth and especially the fifth reps (they are pretty high) it looks like your back is rounding. You want a neutral spine. Your back should be flat throughout the rep. Make sure you take a giant breath, hold it and squeeze your trunk muscle tight with a neutral spine. That might be the source of your hip pain.
You might think about getting a belt soon.
In my experience shoulder pain while squatting is caused by your grip on the bar. It is hard to tell whats up from the video. It looked like you might be moving the bar around between reps. Your elbows slightly move up and down. You dont want any slop in there between reps. keep it tight.
These videos might help you figure out whats what with your shoulder and grip:
The Squat - Bar Position with Mark Rippetoe - YouTube
Squat Grip Correction | On the Platform - YouTube