Anybody who's seriously interested in this subject needs to get hold of a copy of the Nautical Research Journal for Summer, 2015 (vol.60, no.2). It contains an article titled "What Did HMS Victory Actually Look Like at the Battle of Trafalgar?" by John Conover.
I confess this is my first acquaintance with Mr. Conover, but he knows what he's doing. He shows us no fewer than eight drawings Turner made when he went on board the ship after the battle. They reveal a wealth of interesting stuff. He also addresses the "block model" of the Victory, apparently made during or after the ship's 1802 refit (and now in the National Maritime Museum, Greenwich).
At the end of the article Mr. Conover presents a small, computer-made drawing that shows what he thinks the ship looked like in October, 1805. The most noticeable characteristics:
Shoulder-high, unornamented bulwarks around the forecastle - with three gunports on each side. But no bulwark across the forward side of the forecastle.
Boarded-up hammock nettings in the waist.
Shoulder-high, unornamented bulwarks on each side of the quarterdeck, with five gunports on each side between the main- and mizzenmasts.
Boarded-up hammock nettings around the poop (but not across the aft end of it).
An additional cheek knee on each side of the bow, bracing the knee of the head.
No entry ports.
Frankly, to my eye at least, the ship in Mr. Conover's drawing is nowhere near as attractive aesthetically as the ship I've seen at Portsmouth. But I believe he got it just about right.
I have the impression that few, if any, participants in this Forum are acquainted with the the Nautical Research Journal. It's been published since about 1947 by the Nautical Research Guild, and it can reasonably claim to be the best American magazine about ship modeling - and quite a few other maritime subjects. Membership (including the magazine subscription) costs $48.00 per year. For that you get four issues of the Journal, and lots of other benefits. The Guild holds a convention every year (each time in a different part of the country), and those conventions are a blast, with presentations by modelers about all sorts of subjects, a banquet, vendors, etc. (Rather like the IPMS conventions.) The Guild maintains a lending library of most of the important books on ship modeling and the history of ships, and will ship them to any member who asks for them. The Journal contains articles about prototype ships and boats, model construction, queries and answers, etc. Each issue has a section of book reviews. And, for a surprisingly low price, you can buy the entire run of the Journal since its founding on CD-ROM. A priceless source of information and ideas.
Highly recommended. If interested, go to www.thenrg.org.