I thought this was pretty ambitious! A big world & customization is pretty insane on a 96 hour crunch. I think the mechanics of gathering resources and upgrading your sub should definitely be used in any of your future projects!
Personally, I would have preferred if the player started with the storage module installed. I got kind of frustrated driving (sailing?) around the map for a few minutes being unable to pick up items. I hadn't actually realized the shipyard was there for a little while. But maybe that's just me.