Rich-
If my memory is correct, do a search on this site and there will probably be several postings. Cleaning up the original adhesive, masking the inside of the window, and building a wooden support mounted on the stanchions with arms pressing against the plexiglass were crucial points. I don't recall the recommended adhesive to use.

Sikaflex 295 in white or black is the only version that that manufacturer recommends for sticking acrylic to aluminum if you are doing hatches as well, but their recommended primer was worse than useless on the aluminum (like a black paint that peeled right off). 295's efficacy on acrylic to fiberglass with no primer was OK, but I screwed up by NOT building the wood frame across the stanchions. (I thought i applied sufficient even pressure with a length of 2x4" and trucker straps, but it left gaps in several places leading to multiple efforts to reseal due to ongoing micro-leaks. I will still need to apply more Creeping Crack, but it leaves stains on the outside that are tough to remove.)

I further messed up by finding that the original SS screws were so short that 95% of them had not actually engaged the fiberglass, so I did not have the plastics workshop drill the many holes around the edges of the acrylic for me to replace the original 1/4" screws with 1/2". Doing so would have solved my self-made problem by pulling the acrylic in tight to the fiberglass, but then building the wooden framework also would have done so.

The original porthole acrylic was OK for templates (mark the port/starboard and inner/outer sides for the plastic supplier) even though I broke a couple during removal. Scraping off the original glue is tedious, but doable and you can buff off the last bit with a power tool. 

Careful masking tape around the final adhesive application and the use of firmly placed wood pieces jammed against the new acrylic should lead to good results over 24 hours, even WITHOUT buying and pre-drilling new screws all the way around each piece. (If you are doing this while the vessel is in the water, the pieces of wood could pop out if she is rocking in waves over the 24-hour drying time.)

NOTE: afterwards you have to be super careful to never let Windex get close to the acrylic. I have a couple of spots where we've allowed something that must have been similar to Windex drip over the new acrylic and crazed it again. The crazy does not go all the way through the plexiglass, it just affects the outer layer.

Catalina uses Dow Corning  795 Silicone Building Sealant.