I've done some reading and I agree with you re the butyl tape. I would be interested to know what it is you have found as an adhesive. \
I understand that the the fiberglass and plexiglass expand and contract at different rates and the adhesive needs to be flexible enough to accomodate both.
South shore yachts recomends an epoxy
(MS590) that they say does that and I have found it from a wholesaler for aprox $50 per 40ml tube. SS says you need 1 tube per window. Unfortunately you need to buy the material from them (SS) to get the instalation instructions they offer but they're too pricey for my budget It also requires the use of an epoxy
mixing gun which I have found for about $70.
I have already removed the windows and dropped them at a fabricator, I can get the windows fabricated in 3/8 plexiglass/acrylic (which is what they are) for $135 per window(not smoked) . $$$$$$$$
I can't really save much by skimping on the material so why take the risk of having to do it again????????
I have an article on port light replacement that is fairly detailed so when the material arrives I guess I'll give it my best shot
I will let you know how it goes and pass on whatever I learn
Hope to chat again