As you probably know, the hardtop window seal is L-shaped. It should be glued in using an appropriate weatherstrip adhesive. I'm partial to the 3M brand. Use a plastic shim to push the seal into place. I've used a Kleen-Strip plastic stripper (from the Home Depot paint dept) successfully in this type of application. I would start in the corner and go out from there.
Dry-fit the seal first to see if you'll need to trim it at all. This doesn't mean that you have to cram it into place, just lay it on to check for fit. Make sure that you remove as much of the old adhesive as possible.
I haven't replaced these seals before, but I have replaced every seal on the soft top.
Your window should be adjusted to fit the soft top. The hard top should then be adjusted to fit the window. This thread has information on adjusting the hardtop.
Can't get the Hardtop on Tight!