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.