DISCLAIMER: I AM NOT AN EXPERT
from the OP: what is the goal? if it's to have a '49 Ford woody, couldn't you leave the body intact, remove the trunk lid, and graft just the roof section from the '49 Mercury? you'd be left only filling a wedge from the beltline to the top of the rear fenders.
sounds like you're no stranger to cutting & fabricating, so the interior tub won't pose much of a threat.
then overlay the door & side panels with some .025" styrene strips to border your panels and fill in with faux wood or decals.
i guess you're cutting across, and i lengthways