I'm not sure this is a good idea. If I'm not mistaken there are cross bars going across under the roof and above the head liner. This I believe is the reason some folks haven't shot for the VXo2 look due to stability reasons. Besides, most of the marine windows are Plexiglas from what I've seen. Plexiglas on the roof isn't gonna last that long.

Also, any cut metal should be prepped, primed and painted ASAP after cutting!

It's your VX though, have at it if you like