Got my top put back in. repaired the push rods with new ends, got it adjusted and it works fine but this clamshell fit is really annoying. For some reason the clamshell seems to be hitting the top on the drivers side keeping it from closing all the way. I don't think I could of put the top in wrong because it has 6 bolts that go into non adjustable holes. So I don't think that's possible. I did retape the back of the top with 3M tape. Maybe I got it too tight on that side but it doesn't look like it. The top seems to be too far back on that side. The edge is not sliding over the rubber bumper on that side as it is on pass side. It fit perfect before. Here's some pics. Maybe someone has came across this before.
The gap:
Passenger side edge:
Drivers side: