I didn’t find this information anywhere, so here it is for the Google archives…
To get Prototype to run after squeezing it through ShrinkSafe, you need to put back every instance of the variable $super. ShrinkSafe replaces variable names with shortened versions, and because of some Prototype voodoo, it breaks on this one name. There are about 8 places you’ll find it, and unfortunately, it takes some manual hunting once ShrinkSafe has changed a bunch of names, but there you have it.
I suppose someone smarter than I could tweak ShrinkSafe to ignore this variable name, but for me, this works.