Sorry about the delay in responding, between Hershey, fixing the Leatherback and just general life the Fordbarn has not been regularly addressed! Did look for messages, but that's all.
The instructions for the top from the manufactures called for the cutting of the top material to within 2" of the edge of the window frame. Then use a heat gun or hair dryer to pull the material in till you can tack it on the inside of the frame. Due to the weatherstripping around the glass itself you can judge just how far inside you need to be before the rubber helps seal it. The instructions note that you may have to make small radial cuts in the material to make the rounded corners. We made them very slowly and carefully. As I said before however, make sure your wood window opening is smooth and today I would even route a small round-over in mine to make the pulling go better.
Good luck