I have replaced a couple of inflatable transoms. A lot depends on the material at the junction of the PVC fabric and the plywood. Some have a very heavy and thick plastic, and on that the only thing I found that worked was 5200--that was awkward to clamp. If I had been doing it over, I probably would have used bolts to hold the vinyl in place. Or cut battens and a couple of screws--fill with epoxy later. We didn't have G Flex then--and it may well work.
Be sure and cut and bevel the wood exactly as it was before. I found that there was sort of an "S" curve to the cut out for the pontoons. Each boat design will be different. You also want to epoxy soak any open edges of the plywood before assembly. I would coat with epoxy any holes, such as the drain. Be sure and wash off amine blush as well as light sanding before using another epoxy or coating on the plywood where epoxy was used.
The HH66 will work very well on the PVC. I did some destructive testing when we made the side curtains of Shelter Rite for the current C Dory 25, and the material failed before the glue. If you need to thin it, it is probably best to use their "Thinner". I tried to mix my own--it worked fine, but real MEK is getting difficult to get---and there is a "substitute" which does not mix with the HH66 well. Also be sure the glue brush is tight in the cap. I have had them come loose.
Great project we would love to see some photos. You may have to put the photos in an "Album" on the internet, and then link to that. The format has to be one of the standard photo conventions such as JPEG.