I know I'm a little late, but....
Yes, I still had to comment on this story. It's a great view on things. Like you, I have been wondering how little Kal-El had survived his trip. The diaper thing as well as the feeding question have crossed my mind on more than one occasion. And the bathing thing.
I sure love your take on this. At first, you had me terribly confused, as I suspected it's Martha speaking. I then reconsidered to Lara and even Lois with the baby they found in the fourth season. While reading it a second time, I finally realized what was going on, though.
The whole idea of a space ship with feelings is great and original. What I still don't know for sure, though: When the ship feels darkness surround 'her', is it because 'she' dies, or because 'she' is buried by Jonathan? He did bury the ship somewhere near the farmhouse, didn't he?