You can replace the ship (and any other) with any other of your liking by modding the file placedobjects.xml in the (unpacked) md folder. Concerning the Duke's Buccaneers quest there are many useful resources, for example this Confluence walkthough. But this is a question better suited for the X4 main forum as it has no relevance to Scripts & Modding.
And for any future posts, please do not use spoilers in the title and use spoiler tags in your post.
Cheers Euclid
"In any special doctrine of nature there can be only as much proper science as there is mathematics therein.”
- Immanuel Kant (1724-1804), Metaphysical Foundations of the Science of Nature, 4:470, 1786