Hi Geo tracker2.
When I installed my hardtop on mine (originally a softtop) I never removed any weatherstripping. I found some silicon spray on the weatherstrip helped it slide together easier. Pushing from the rear gate to wiggle it on. The weatherstrip on the vehicle sits in a channel on the top and needs patience to get it to fit together. I remember swearing and cursing when I did it by myself. Once I got it on, I never removed it. Try the silicone spray, it will help everything slide into place much easier.
Also, the front targa piece. I had to make spacers out of plexiglass to lower the front latch anchors by the windshield. Once I switched to the hardtop, it wouldn't latch properly. By making the spacers, It snugged the top down nice and tight into the weatherstrip.
Hope that helps.
Technician
Licensed Interprovincial technician in Canada. Well versed in Suzuki, Ford, GM.