cbloom, zercher squats might be a decent alternative to the hacks (i've never had shoulder problems so this could be terrible advice, but its worth a try). i googled them and found this illustration, not great but it gets the point across.
http://www.abcbodybuilding.com/exerc...rchersquat.htm
I'm interested to see how all you guys do on this program, never heard anything about it before.