I have sone rust spots along the top of the windshield/roof and wondered if there was a way to remove that seal without removing the window all together.

The seal comes off separately. I've helped do 2 windshields on my 1G's and the seal comes off first and goes on last after the windshield has been replaced, so you can pull it out. But you will more than likely need a new one after and need to glue it back in place. My old one was never reused

You will have to replace it if you pull it. But any windshield should be able to get you one.

Hey Kirk, what did you decide to do here, I am on the fence about pulling mine and am leaning towards doing it after reading this. what did you do?

I left it, got as much surface rust off as I could and painted it will get redone if i get it painted.