It's a 'thought experiment' as my philosophy professor would say.
I wouldn't say in Story 1 that the Ship of Theseus is the SAME ship as it was on Day 1 as it is on Day 3002. I think it's still the Ship of Theseus, but because it has undergone such a physical transformation it can't be the 'same' one. And for story 2, same thing, it's not the Ship of Theseus. It's just another ship made up of the old used parts of the Ship of Theseus. I think their identities mean more than their parts. It also has to do with the history of the parts and the event of building the ship as a whole. The first Ship of Theseus was built for a voyage and for Theseus. The second Ship of Theseus was built by some man who couldn't afford his own parts and I'm not sure what the reason for building his was.