Dread Pirate Wesley,
Let me start by saying this is a really fantastic build and I have greatly enjoyed following it VERY closely.
I am new to this forum and currently trying to make my own sailing ship so I found this build log fascinating and informative.
I have a few comments which you have likely already considered, but...
First, the proportion of the hull is not right, in that there is way too much ship sticking up out of the water relative to its length. You have the bulk of a 3 decker. But the 64s and even 74s were "thinner" in appearance.
Secondly, and this relates to point 1 in a nice way: your lowest black stripe running the length of the hull should be much wider than the upper black stripe. If you simply removed 1 brick height from you upper black stripe you would lower the height of the hull side while correcting the stripe issue all in 1 go, though it sounds like that would ruin your deck height engineering and minifigs would no longer fit!
Third: You addressed this early in your build log, but I still think there is something not right with the angle of your hull sides. Particularly at midship, nearly the entire hull side should angle inward all the way to the top. The angle changes along the way, but its all "leaning" inward.
Fourth: I realize a lot of people go with that bright yellow for the yellow ochre paint, and Lego doesn't give us a good choice with color. But it is just so bright and garish. Have you considered "brick yellow" or "tan" as a substitute? It wouldn't be right either, but it would be more muted and perhaps not look so toy like. I don't really know about this! I am just kicking around ideas here.
Lastly, there is something that does not seem right about how your hull goes straight down into the "water" at the very bottom of the ship. At dead midship, that is probably accurate, but the ship should be angled inward fore and aft in particular, and really only a small portion in the center of the ship is reasonably "straight" or vertical at the waterline. There is an excellent photo of HMS Victory at sea, taken around the year 1900 I believe, at wikipedia. Look at the angle of the hull as it meets the water from bow to stern. There is something that just seems "off" about having the ship go straight down to the water line. I would consider lining the entire bottom of the ship with a row of inverted slope pieces, so that the ship slopes inward, away from the viewer, at the waterline. Or you might want to recess the bottom by even a half stud (plate) followed by another half stud recessed plate. The slope would be much more gradual than by using 45 degree inverted slopes. If any of that makes sense! This also might be one of those things where even if it is technically "correct" to have the ship meet the water vertically, it still doesn't seem right to my eye. It seems like a slght angle (inward) makes sense, even if done as a "creative trick of the eye". These huge ships just didn't meet the waterline in that perfect right angle kind of way.
I offer all these comments as just that: comments to be kicked about. If your ship wasn't as brilliant as it is, I would probably refrain from commenting at all. But you have a real chance here to come up with something truly magnificent (it's practically there already!) so why not go all the way? I'm curious to hear your responses to some of these thoughts, as you have very clearly spent a great deal of time, effort, and money on this wonderful build!
I hope to post photos of my own build (probably stealing some of your own techniques!) in the near future.
Keep up the OUTSTANDING build!
And keep your powder dry!