TMJB,
My experience and process for this project last year was very similar to what Paolex describes - with a few variations which may be helpful to you or others.
I had the same issue with the fit of the trim rings. Solved with the use of a small finish sander on the offending inside edges of the trim rings. I also had a few places where the cut out for the angled drain spigot was not deep enough at the outside face of the cabin top. A half inch diameter hasp fitting on my electric drill took care of that.
Some of my plywood core was damp, but I had the luxury of letting it dry out under shrink wrap through an exceptionally cold dry Chicago winter. Pulled the old portlites out in November after the boat was shrink wrapped, taped plastic over the openings with shrink wrap tape (Not masking tape.) top and sides to shed any water dripping through the shrink wrap at the rigging penetrations, left the bottom edges open for air circulation, placed a few Damp-Rid buckets in the cabin, and it was all bone dry by April when I put the new portlites in. I sealed all my plywood core with penetrating epoxy to protect it against future leaks. I personally think that the epoxy sealed plywood edges may provide a better bonding surface for the silicone than raw plywood, which can be kind of "fuzzy" for lack of a better word. I absolutely believe that plywood or balsa core should be sealed with epoxy at all penetrations. It's cheap insurance and doesn't take long to do.
Some of the original cabin top cutouts were unacceptably sloppy. The openings were tight in some places and so big in others that the screws had no bite into the plywood core. Since there was pretty consistently about a 3/16" gap between the cabintop and the interior fiberglass liner, I was able to epoxy in 3/16" x 1 1/4" strips of plywood reducing the effective opening size where needed to provide positive grip for the screws. I enlarged the openings where I did not see space for at least 1/8" of sealant between the portlite frame and the cabintop. Lots of test fitting. There where some hollows in the plywood core which I filled with thickened epoxy and there were also a few screw holes on the new portlites that where not in same location as the originals.
I used the Dow 795 structural silicone recommended by the portlite manufacturer. It's not ordinary silicone caulking. It's professional grade sealant used on building construction joints, and can be used in pretty low temperatures. You will not find it at Home Depot or the other big box stores, and West Marine has no idea what it is. Have to buy it on line or from a construction supply wholesaler. The outfit I found on line was called Mudd Supply. The price and delivery time seemed reasonable and they had the quantity I needed unlike the various eBay and Amazon sellers I came across selling just one or two tubes.
One great tip given to me by my yacht yard guys was to use masking tape liberally. Fit the portlite in place with a couple screws and mask every face of the portlite and cabintop where you don't want the silicone. Then pull the portlite, put a generous bead of sealant along the bottom edge (No sealant on the inside flange.), slide the unit in and down, put all the screws in, then inject the sealant around the top and sides from the outside, additional at the bottom if needed, work it in with a putty knife on all four sides to insure there are no bubbles or gaps, then scrape off the excess and pull off the tape. That seals the portlite to the cabintop. Repeat the same process with the trim ring. Maybe not necessary, but I also put a bead of sealant between the trim ring and the portlite thinking of that as an additional line of defense since the trim ring is already sealed to the cabintop with the same silicone. The masking tape saved a lot of clean up time and the results look professional.
I did all the work except the final install of the trim rings crawling around the deck under the shrink wrap, protected from the weather. I am happy with the results, no leaks the first year, fingers crossed for many more leak free seasons. Don't want to do it again anytime soon. My knees and back felt normal again after about two months.
