:... However, at the stern it doesn't look so
: good and my wrinkles are actually at the keel, not up by the chines where
: it wouldn't matter so much. I guess this must have to do with there being
: a bit of rocker in the aft region of this kayak (not really intentional,
: it just worked out that way). I took out a bunch of the staples to try to
: work the wrinkles out from farther back but I'm not sure it's helping.

You can slice open the skin that is loose / wrinkled.. cutting along the keel
centerline , overlap and glue the skin where possible , and then cover the
incision with a rub strip. Think of it as an extension of covering the
stems. Or, you can ignore the wrinkles and go paddling

The PVC you are using can be part of the problem.

Tom