Installed new roof on 2001 Boxster and now the windows won't close correctly

[Jasper7821]

Roof was just replaced and not closing properly
When the windows come up the passenger doesn't clear the rubber seal and goes down 4" or so. If I close the door then roll it up, it'll close and get stuck there. I can stick a screw driver in and push the seal inside then the window will move just a hair up and close fairly enough.
On the driver side, the window doesn't go on the inside of the plastic top window frame on one spot. I can push the window there and it pops in the channel.
Even with them closed like that there's still gaps and wind noise.
Everything worked fine before the new roof (could use a new regulator) so I think it's an adjustment.
Just looking for advice on what to adjust.