The top window frame is being flexed too much. Needs one more cut ! The new cut can be seen at the right end of the white filler strip.
Here's a picture of the inside for the record.
The windshield set into position with an 8mm slab-o-plastic holding up the roof.
The "B" post is straight from the PT, just trimmed and  repositioned.
Last photo before putty.
The ugliest part of the project is always the putty. Right side of the car turned out right. The left, I wasn't so lucky. The roof was low.
If it needs filler, then add filler, don't just keep sanding away. I use a black finger nail sanding stick from a dollar store.