Because I worked hard to make sure that both bulkheads would land exactly where I want them, I decided that it would be a good idea to glue them in place with lightly thickened epoxy before I make the very thick epoxy fillets and then apply fiberglass tape. This is not in the Pygmy hatch and bulkhead instructions, but I don’t want there to be any chance that I might accidentally push them out of position when I am applying the fillets or bedding in the tape. Also, since the only way that I can reach far enough into the cockpit and hatches to reach all areas of the bulkheads is to turn the kayak on its side, I worried about bulkheads flexing out of position as I turned and strapped the kayak. I can now put that worry behind me. This will add several hours (perhaps a day) to the process while I wait for the epoxy to cure enough that I can go back and start on the fillets, etc., but I think it is a reasonable precaution.
EDIT: I have decided to wait until tomorrow to resume working on the bulkheads. I want the epoxy that I applied today to be fully cured before I start doing the fillets, etc. It won’t hurt anything to wait, and it is cheap insurance, as the saying goes.