How should the rear roof seal be aligned?
I have one from 914 rubber and if I align the inside lip with the roof inner edge therhick fuzzy part kinda hangs out over the rear edge of the roof?

the fuzzey needs to be in far enough that it sits on the roll bar. It helps if you have the old one to see where it needs to go, but it sounds like you need it in about 1/8 - 1/4".