Want to sail,
Your fear of breathability being an issue is well founded; mildew will build up rather quickly within a stackpack. You could, perhaps, use a phifertex-style material near the bottom to allow some airflow, and that may work
. Or perhaps design it to have an open bottom with straps connecting the sides...but I'd bet you'll still have issues with condensations sitting inside.
$4/yd is good, but one can readily purchase
60" Sunbrella for $12/yd; a stackpack for your boat
would use about 14yds, so it's not too outrageous. Factor in zippers and thread, and you can probably build it for <$200.
As for construction, there is nothing too hairy about it. I suggest building the pack with a full-length zipper that zips from aft forward, and build a uv-flap to cover that top zipper.