Yeah, 15 rep deads would be a killer. The one time that I did HST 15s I didn't do deads.
You're much stronger than me, so I probably shouldn't offer too much advice. I will say this about the squats...I went from less than parallel to doing ATG style and my thighs grew over an inch in about a month. I had to drop the weight drastically, though, to well under bodyweight. Still working back up...
Don't have a problem putting the bar high up on my traps, I use a pad on the bar. If it's shoulder flexibility, there are some good exercises for that. Olympic lifters work them very successfully to get their shoulders flexible for snatches.