Those are in aluminum frames, if I recall correctly.
Some frames are two piece, if that's the case this is easier. You might try to find the original rubber seals, but you can also reassemble the new lenses into the frames (if they come apart) using Dow Corning 795 or equivalent.
Save the old ports and use them as templates to cut new. Use Cast acrylic if you can find it, but that's not always easy.. either way acrylic is preferred over Lexan, which scratches and mars easily. I'd suggest the darkest tint.. it looks best from outside and still lets in lots of light and is essentially clear from the inside (and equally clear from outside at night with lights on below..) Plastics suppliers will usually cut it for you for a small fee.. generally worth it.
If using a sealant rather than gaskets be sure to mask the exposed areas of the lens and the frames carefully to ease cleanup later, lay the sealant into the frame halves, (use several small bits of the old gasket as locaters to center the lens in the frame), wipe up the excess and reinstall the frames. Remove the masking and 'voila'!
If in fact the frames are plastic you may have more issues.. they rarely survive removal intact, but you never know.
The other alternative is to apply new ports to the outside surface using the same sealant.. here you have options too, screw/bolt in or simply use the adhesive sealant as a glue (cleaner look but you need to rig something up to hold the windows in place during the cure. The same sealant works a treat. This also gives you the option of slightly updating the look with perhaps a slightly different shape since you're not constrained by the cabin cutouts anymore. It also means you'll have some dressing up to do below where the frames were.
If you go that route, be sure to drill oversize holes (if screwed down) and plan a residual thickness of sealant (both to allow for expansion differences between F/G and the acrylic.) Again carefully and fully mask all adjacent surfaces for easy cleanup and a crisp look afterwards.
It can look OK even with screws.