Your rear window frame is likely to be distorted a little. This happens after years of vibration and it will make it difficult to re-install the rear window.
If you are doing a new top then the window frame will be off the car for a while. We recommend that you do a trial installation of the rear window, off of the car. Wrap the seal around the glass and lay it over the rear window frame. Re-shape the frame until the glass "seals in" well (at the workbench.)
Our integrated rear window frames eliminate this problem. They are the steel plus the wood tacking frame, in one unit, ready to tack into the new top. You will find them at "Convertible Rear Window Parts."