There is an overhang of the lower seal but should seat against the body. I have a little sliver of a gap in mine looks fine.
To get the windshield back to its original angle you have to a few things. The spreader bars have a long bolt that can be used to draw it back. If it won't move nicely you can use some ratchet straps to draw it back using the roll bar main beam as an anchor.
If you can get the spreader bar bolts started you can tighten it up till it quits let it set over night and try some more in the morning. If it still won't go buy a package of the straps and use some blankets to protect the paint and get to rigging it up and ratchet it back along with the spreader bar bolts.
It will definitely piss you off at first but all is good it will come back to where it belongs. Play some hard rock and have a few beers your YJ will love it and go back to normal real fast.
89YJ 2.5L TBI, AX-5, NP231 SYE, Ford 8.8, Yukon Grizzly, Tom Woods Shaft, 33" BFG T/As, 4" lift, Warn VR10000s.
AF Jeep Club Tail #184