So many issues
First, it would need to be a Transmutation spell
Yes, there may be skeletons involved, but really, the spell is fixing a ship. The fact the skeletons exist is beside the point. The fact that a whole new ship can be created might even put in the realm of Conjuration.
Where is "30 feet of the destruction/sinking site"?
Thirty feet from the bow? The stern? Do you need the exact GPS coordinates of where it started sinking? Speaking of which, what if the ship moves while sinking? Is it where the ship started going underwater or where it settled on the sea floor? What if the ship broke in half and sank in two different directions? Far too many unanswerable questions to have the caster not be in contact with the ship in question. Make this a Touch spell. Yes, that means breathing underwater and possibly losing the Verbal component.
On a different "30 feet" tangent; if you expect the caster to be above the ship while casting, what happens to the craft they are on when the ship rises? I see a situation where the caster hires another ship to bring back the first, and when the ship "rises", it crashes into the second ship causing it (or both) to sink. Or do you expect the caster to just be floating on some debris for the two hours of spell casting? Look for rules on Hypothermia.
Components are questionable
What do you mean by "wood akin to what the ship was made from"? How would the caster know what went into the construction? Or once again, are you expecting the caster to be floating on a chunk of wood from the ship and that is part of the components?
What do the ten copper represent? Is it an expense? Otherwise, the whole thing can be cast using an arcane focus. No wood or sail needed.
Duration is either Instantaneous or Until Dispelled
Both would mean that at the end of the two hours, the magic instantly happens. With "Until Dispelled", it has the added factor of some other caster casting dispel magic and re-sinking the ship.
Spell lists are for what makes sense, not who wants it
There are plenty of spells that are on the Wizard list that I'm sure other classes would love: Wish, Simulacrum, Bigby's Hand, Find Familiar. So don't make the list based on who wants it, but who is capable of that much power.
So Wizard, maybe Warlock, maybe Storm Sorcerer subclass, and maybe the Circle of Land Druid subclass.
Who "owns" the ship?
You mentioned in comments you thought about only the owner being able to cast the spell (or have owned it). Does this mean that the spell caster is the only person that can claim ownership? What if it was bought by the fighter? What if the caster used to own the ship but sold it/lost it gambling? What if the ship is owned by a benefactor that is letting you use it? What if the party commandeered the ship while it was docked? Does 9/10th of the law work in the FR? The term owning/owned makes it weird about who can and cannot cast the spell.
What happens to the cargo?
What happens to all the food, water, gun powder, cannons and cannonballs, personal belongings, maps, etc? All of which could be ruined, washed away, or both. I mean, great, you have a ship again, but all the food and water is worthless, and good luck defending yourself with wet powder. Hope you can make dock quickly.
And now for the shenanigans!
As stated, the ship rises from the ocean. This can be a war tactic in waiting for a ship to come this way and finish the spell right as they are passing overhead (or put out a decoy to make them stop for a moment). Old ship rises, and BAM, crushes the new ship.
If things look bad, it makes more sense to sink your own ship! Unload the cargo, blow the ship up, then ten copper and two hours later you have a completely new ship! Everything would be a bit wet, but small price to pay, right?
My favorite; the description says that when the ship rises, it comes back with 2d4 souls to man the ship. But it doesn't say anyone had to go down with the ship! So take the ship into a harbor, sink it, raise it, and now you have a crew that needs no food, no water, and no pay. Not enough souls? Do it again! Skeletons don't need to breathe and would likely survive the dunk so the next casting will add to the crew. The description says these skeletons cannot attack, but I would put them to work priming the cannons, steering the ship, bailing water, and any number of tasks while the party takes Attack actions.
And to build off a few of these; what if the party WINS a sea battle? They can (1) bring all the surviving enemy crew and booty on board, (2) claim "The ship is ours!" and then promptly sink it, (3) send the Wizard out in a rowboat for two hours to cast the spell while the party boat floats to safety, and (4) raise the ship with a faithful crew of skeletons! Now you have the beginnings of a fleet! Given a little time the party will have an armada of ships helmed by the undead.
Don't think about the party losing the ship, think about ways to save the ship!
- Spells to fix holes in the ship (like creation)
- Spells to replace cannon balls (or make them more powerful like the magic stones cantrip)
- Spells to bail more water than create or destroy water can normally handle
Hopefully you get the idea. Don't let the party get free ships, make them work to save the one they have.