On Wednesday I ground the new glass close to flat and flush, using a straight edge to find and mark the high spots. 
I got to wear my new Wes Cravens designed grinding outfit, hoping to mostly avoid the infamous fiberglass itch.
Next followed three cycles of filling the low spots with Microlite putty and fairing it flush and flat with the manual sanding board (torture board). A foot-wide $3 plastic smoothing tool was a great help in applying the putty flat and smooth across the entire area.
The rain predicted for Thursday was delayed, so I was able cut out the holes for the new ports using my big hole saw and new jig saw. As anyone who's done it will tell you, cutting big holes in your boat, even above the waterline, is always traumatic. "Measure twice, cut once" was a mantra I repeated over and over. Careful use of drilling and cutting guides helped it go smoothly.
Cut-outs showed that my laminations were good: no gaps, all the mat layers fully saturated with resin A little grinding to round the inner edges and the ports slid into the new holes perfectly. Whew!! I coated the newly-exposed edges of the plywood interior liner with epoxy so it wouldn't absorb water and rot in the event of (Heaven forbid!) a leak. While I waited for the epoxy to cure, I cut and applied butyl tape to a porthole flange. In addition to the flat cut pieces of butyl around the outer flange, I added a strip around the corner where the inner and outer flanges meet at a 90 degree angle. The theory was that it would squeeze out between the inner flange and the edge of the hole, resulting in a good seal. 
The epoxy around the hole on the sunny side cured quickly enough for me to try to bolt in the port. I soon discovered that my newly-purchased bronze machine screws were too short to extend through both the uncompressed butyl and the mounting flange. Damn! After a few moments of high anxiety, I thought I might be able to use a couple of clamps to compress the butyl enough to get the screws through. By repeatedly clamping and reclamping around the perimeter and using a lot of clamping pressure, it worked like a charm. 
The individual butyl pieces welded to each other nicely, and the excess squeezed out between the flange and the hole as I had hoped. 
Of course some also sqeezed out around the inside mounting flange on the cabin side, but that was easily removed simply by cutting around the flange with sharp knife and lifting off the excess.
At this point, the epoxy around the hole on the shady side still wasn't cured, it was getting late, the rain was coming in, and I was beat-all good reasons to call it a day and head home.
It rained Friday and Saturday, so I continued with the shop projects. I rounded the corners on the mast support post cover, cut matching bungs from scrap jatoba and glued them in place on one side. 
On the other side (the piece that will be screwed on during installation) I mounted a teak grab handle. No, I didn't make it. At twelve bucks (even at Worst Marine), it wasn't worth the time. 
The next morning, after the glue had set, I trimmed the protruding bungs flat using a flushcut saw. 
I find it works better than using the usual chisel method. Even with a sharp chisel and thin cuts, I usually end up with some of the bungs breaking off below the surface. The flushcut saw doesn't scratch the surface and results in the bung trimmed so close to the surface that normal finish sanding is enough to make it perfect. Finally, finish sanding of the post cover pieces, and between-coats sanding of the varnish on the table parts. Last thing Saturday was to apply varnish all around.
Sunday was a beautiful day. I installed the second port as I had the first and applied a bead of 3M 4000 UV around the ports to finish off the installaton and create a redundent outer seal. 
With some white plastic caps to cover the protruding nuts and bolts, it will be a pretty clean installation. I cleaned up the week's mess (well, mostly), and called it a good week.
