Well, let me clarify a bit on the matter of the Windwright Captain and our need of a pilot; I would rather play the Knight Phantom. What I'm saying is that I'm willing to jump on this grenade if no one else will lol.
And Zaer, Windwright Captain requires 6 ranks of UMD, which means without at least 1 level in a class that has UMD as a class skill you can't qualify by 8th level. This, in turn, limits the number of classes that qualify easily/naturally. If I've found all of them, the list goes Artificer, Bard, Beguiler, and Spellthief.
Now, just about any other Arcane casting class can qualify by 8th with a Rogue dip. If I were to roll up the pilot, I'd probably do a Half-Elf Spellthief 1/Duskblade 6/Windwright Captain 1.
Also, for your GMPC, I highly recommend the Legendary Captain PrC. I was gonna mix it with Windwright if the former didn't require that the character be master of the ship.