... I realize I was pretty vague.
Please understand that I've been posting about what I would have done and not what you should have done.
You crafted a wonderfully evocative hook which lead to an exciting adventure that resulted not only in your players "earning" a ship but also in your players having a great deal of fun. That's a win by any measure and we all should be so lucky in our own games.
All the questions about "operational familiarity" after 300 years and questions about what condition the ship was in are just the posters here tailoring your adventure to their groups' specific needs. No one ever runs a module entirely as written. We always tweak something, add something, or remove something as we tailor the materials to better "fit" our games.
We're taking a suit off the rack to lengthen the sleeves or take in the shoulders so it will better suit our frame. The suit is so good that we want to wear it, we've just got to make it fit first.