First off, thanks to all of you for the comments so far. :-)
Now, to the questions.
Sir Dillon, it is indeed an optical illusion. The center mast is (and should be) the tallest of the three, however by only a single brick height, for which I can understand some confusion when looking at the ship front on.
Mr. Berry, I agree the cabin does somewhat stick out. It was something I kinda/sorta noticed as I was building, but I wanted to finish the ship and see if anyone else thought that as well. What kind of ideas do you have to detailing the sides?
Mr. Tiber, the Corinthian did indeed donate the hull and a decent amount of the parts to the Marathon. Again, I do see how the cabin is blocky, I was hoping the slanted back would help some with that. Any reccomendations on how to fix that? Oh, and you can probably expect another ship sometime in the future, although I'm not sure if it will be as big as the last two.
Mr. Bond, I agree black are more realistic, so I will use the excuse that a crewmember got bored one day and wanted the lanterns to be prettier. :-D I think being taller would make it stick out more, so I guess its back to the whole blocky thing.
God bless, Sean