Yeah, that Low Bar can beat up the front of your shoulders.
1) At last it's not in your elbows - that really sucks
2) It will go away to a degree, but you'll see it show up in your Bench performance.
3) Rotate Hi Bar and Low Bar...maybe invest in a Safety Squat Bar.
4) I forget, do you compete? If not, don't kill yourself to do Low Bar. Have fun...