I've heard both that the little metal pins need to go and that they can stay. I'm thinking it might have to do with different brands of rubber trim, but it could also be installer error or something else. so I cut them off just in case for the 88 I'm working on when we got the glass replaced.
do not expect to reuse your current windshield. the old glass is INSANELY easy to ruin when you try to remove it. bonus points is that the rubber trim is free if you order new glass for a 97+ XJ. super bonus points is that you get brand new glass to see though!
do plan on finding surface rust where the urethane needs to bond to the steel. very common and the glue won't adhere properly unless it's addressed. if it's too cold where you are for painting, I'd probably wait until spring to do this job.