Yes- It seems they can't fit through the cabinsides. When the boat was built the installers would let the channel in the port extrusions ride down into the cabin's port aperture and then slip the top in too. You'll need to get all the adhesion of previous calk taken care of and then make sure all the calk is removed so the cabin side will fit down
into the ports channel in the extrusion.
For a better-than-new job, shim the gaps between the cabin side and hull liner to match the biggest existing width dimension. This insures an even fit for the ports inner clamps to operate correctly. Add thickened epoxy to the gaps and bond the cabin to the liner. I used matchsticks for the spots where the distance was too small. After the epoxy cures pull the sticks and fill again the remaining holes with more thickened epoxy. This gives a nice solid, even and crush-proof aperture to mount your ports into. After I did this I ground the apertures to fit the ports extrusions without tucking them down into the frame extrusion. This made a perfect mate between the boat and the port. I used simple Home Depot 20 year silicone calk and that was 12 years ago. Today hatchmakers sell a Butyl Bedding that I haven't used but many pros use.
http://www.newfoundmetals.com/catalog/pg09.html Dry fit the ports and mask around them. If you are thinking of painting your "Bandit Stripe" now is the time to do it.
Remember the boat cabin has a camber and the glass frames do NOT! You'll want to allow for this with your calk of choice. Let the middle of the port be close and use enough calk to fill the distance between the flange and boat at the ends where the brittle glass cannot follow the contour of the cabin roof. Not a leak since.
Be sure to check the port's plastic gasket that seals the glass to the frame. It or a suitable substitute is available from a local storm-door fab and install company. The frames are held together by small aluminum brackets and self tapping screws. Be careful not to bend the frames while dissembling them. Replace the gaskets and you should have a decade of no leaks from these frames. Many leaks are from the gaskets and NOT the caulk. Don't go through all the work and get a leak from a 30 year old gasket. Remember to install gasket so the joint of the gasket is in the TOP of the finished frame. Laying out the gaskets and letting them settle overnight or more from being wound-up on a roll helps them take the shape you need.
Good luck and Good night's sleep without drips from these gaskets (and frames)!