OK, I sure hope I don't ruffle any feathers with this answer, but here goes.
The high pull is a lift used to teach technique for the Olympic lifts. But the best Olympic lifting coaches prefer the jump shrug. The high pull, done poorly, ends up being more like an explosive upright row. You never want to pull with your arms in an O-lift, so the high pull can actually reinforce bad technique. So if you're shoulders don't like the high pull, then you're probably performing it more like an upright row. And many experts, Bill Hartman included, will say that the upright row is contraindicated for many lifters.
One suggestion then is to substitute a jump shrug. You can listen to one of the all time great Olympic lifting coaches, Gayle Hatch, tell you how to do it here:
http://www.aceathlete.com/hatch/video.htm
You'll need to choose "clean pull" from the video menu.
But maybe you don't really want to learn this lift for a hypertrophy program. How about substituting some type of lateral raise?
Lisa