Yup, my 89 was not sealed well from the factory, but I knew that and kept a good eye on it and redid the chaulk, used a 3M sealant and have not had a problem with it. Problem as to why they rotted was as stated above, the end grain was not sealed well and the only real seal was a vinyl strip that over time would want to pull out, newer Grady's don,t have that, now bulkheads are typically molded with the deck and cabin as one piece, much less work and way less issues.
As for should you use a gap or soft material against the headliner, NO. If you do it will allow the cabin to flex since one side is unsupported, if the cabin itself is 100% perfect shape it should support itself on it's own, but if there is any damage or fatigue, this will really ruin it over time. If I were doing it, I would first fasten it to the headliner with l brackets and then glass over it, this will be the best way to support the cabin as well as making the headliner more rigid and keep it from flexing and cracking. I would through bolt when ever possible and use 5200 in all screw/bolt holes. As stated above, 2 layers of mat would be perfered. When laying mat, roll the wood surface to cover it all, then saturate the mat, more resin is better then not enough, as your roll out air bubbles you will spread it more even and some will come out. Might want to use a resin accelerator to have it cure faster since you will be fighting gravity a little, will keep the glass from wanting to peel off, if done right it won't. Make sure any corners are rolled well and no air bubbles are present, air bubbles are areas that potentially can break and allow water to seep in down the road, and also take away from the strength of the glass/resin. If you missed any, grind them out, but if rolled right there shouldn't be any. To roll, typically start from one end of the glass and work the opposite waythat way all the air bubbles are pushed one way, if you start in middle you will only fight yourself.