Nice work! I've sunk a few hours into this so far, exploring and discovering secrets. Unfortunately I'm here to report a bug or two—the Fighter chassis design screen seems to be broken. I can't navigate past the second Shield slot, it just takes me straight to Done and then loops back to the engine slot again. Since the design screen doesn't fill in the battery slot by default, I can't select Done and exit the screen, so I'm stuck there with no way to bail out and save :( Wish I had saved more recently...
Also, buying the Carrier hull didn't work for me. I had 16 CY and the game still wouldn't let me buy it. I didn't try again with more currency.
Hope you can fix these bugs soon! I'm having a good time with the game on my SD2SNES/FxPak otherwise.