Brian,

I've not built an Merganser 17 but am assuming it's a stitch and glue by your description.

Generally, the build sequence is to wire the hull together on the forms and glue the inside seams with thickened epoxy. Next, wire up the deck on the forms and hull and get all seams aligned correctly.
Then, glue the outside deck seams with thickened epoxy, remove wires, filet the seams with thickened epoxy and sand smooth.
Next, fiberglass the outside of the deck down to about 1/4" of the shear (taking care not to glue the deck to the hull.
After the glass on the deck cures, I then glass the hull using the same concept. Then, you can detach the deck from the hull and epoxy the inside deck seams and then glass....

Bob Beaullieu