I have done a few kayaks each way. I used to cut out the cockpit opening and add the vertical risers before glassing. The last couple I cut the cockpit opening, glassed and then added the vertical risers. That made the glassing slightly easier because the deck is a simpler shape without the risers. I have also glassed before cutting the opening. I didn't find that any of the three different times for adding the glass created any serious problems, but I will probably stick with glassing before the risers are added.

I found the best way to get the edges vertical is some coarse sandpaper wrapped around a cylinder for the curved bits and on a sanding block for the straighter bits. It is easy to keep it vertical as the edge is sanded to the line. I don't own a saw that gives a neat cut, but the sandpaper cleans up the edge and makes it vertical.

I don't use anything to hold the vertical riser in place. I use the heat gun to turn the PVA wood glue into contact cement. I put glue on all the edges to be glued and hold the riser close enough to the deck to apply the heat gun to all the edges at once. As soon as the glue begins to bubble, press the piece in place and hold it for 10 or 20 seconds for the glue to cool. I have never had any move using that method.