I ended up using the same glue to join the transom to both the PVC floor and the rubber housing that sits on each pontoon. Others will probably tell you to use different glues, though. I ended up getting opinions from several sources before I went ahead on mine.
The inflatable material of my boat is made of PVC. I gather most inflatables are made from PVC or Hypalon.
I used a two-part glue by Polymarine specifically for PVC boats. It's very important you don't use the wrong one.
This link on the Polymarine site gives some clues on how to identify whether yours is one or t'other:
PVC or Hypalon? « Polymarine Paints, Adhesives, Parts & Accessories
You also need to buy some Acetone to prep the surfaces to be glued. It's a long, tricky job replacing a transom, so be prepared to scarifice a couple of weekends and evenings getting it right.