Craig,

 

If your bird wasn't pressurized I don't think I'd want to take on replacing the window.

 

But....

 

My windshield cracked in transit from Redmond to Colorado in the back of my Ryder truck.  Of course, the top of the fuselage was still off the airplane and the layups weren't in place around the window either.

 

I was able to remove the windshield with a small pry bar in about 5 minutes.  The Hysol stayed stuck to the fiberglass and made a nice release for the new windshield. You are in luck because you can remove your door and don't have to work inside the fuselage.

 

I would carefully cut the layups around the edge of the Plexiglas and use a pry bar.  Who cares what happens to the window!  You could sand down the layups or leave them there.  If you could get the new window to fit tightly without drilling all the holes to secure it you might be able to save the paint.  Maybe just weight to hold it tight during bonding.  You will likely need to touch up the paint, but even that's easier on the door than the fuselage.

 

If you resign yourself to repainting the door, I would use a heat gun to remove the layups and drill the holes to hold the window during bonding.

 

Mike

 

P.S.  I would guess you got some chemical soaking into the Plexiglas during the paint process.