Thanks, Roger. I ended up cutting it apart today. It never occurred to me that it would be out of alignment because the A pillars were cracked, not completely broken. I was hesitant to put the roof on the car because I'd had so much trouble getting both of them off the respective cars.
I didn't think of using wax paper until now.
I think it would have fit once I took out the wax paper and made good contact with the sealant, but as I approach the 4-year mark of this engine-swap/restoration why not take a couple more days and make it perfect?