Here are some pics of my new ports. There are bigger images in my gallery.
http://sailfar.net/gallery/thumbnails.php?album=73 


The ports were cut out of 1/4" Lexan, cut the same size as the old aluminum frames. I used less than one half 8' x 4' sheet.
I reused the interior aluminum beauty rings.
After cleaning up the old opening and wiping down with acetone, butyl tape was placed around the opening with no gaps, trying to cover the existing bolt holes. The butyl tape was 1/2" wide and 1/8" thick. The seam is was at the bottom and should self seal.
After removing the protective plastic covers from the lexan ports, the ports were placed directly on the butyl tape. From the inside of the boat, I took a small awl and made a mark on the lexan for each drill hole (through the butyl tape). Then from the outside, I drilled through the lexan, slightly oversize (the bolts fit loosely with some expansion room).
Then the bolts were pushed through from the outside after application of caulk into the bolt hole. The bolts were tightened using lock-nuts on the inside. This is a two man job. Tightening the bolts squeezes the butyl tape out both inside and outside. A razor blade was used to cut the excess butyl tape away.
The caulk was 3M Windo-Weld Super Fast Urethane, Part No. 051135-08609. This is available at most auto parts stores. I used 1 and one half 10.5 oz cartridges.
I taped around the ports on the hull and on the lexan port, then applied caulk all around, and shaped it with a tounge depressor (stirring stick). After curing, the excess caulk was removed. For the most part it came away easily using a razor blade to make sure it separated correctly when the tape was pulled.
Inside, I intend to either use caulk, or to push a piece of string or twine into the joint. The butyl tape is sticky and it will smear if you wipe it with mineral spirits. So far I have finished one port by cutting the excess butyl tape off with a razor blade. This seems to be a better job in cold weather, when hot the butyl gets gooey and sticks to everything.
I am not recommending this method yet, first I want to see how it holds up over time. These are well proven materials but time will tell how it works on a boat.
You can see that the lexan is distorted a bit around the bolts, perhaps we put too much pressure on it when tightening the bolts.
The ports seem to be dry. My bilge is dusty, although it usually is.