Wow - that's quite a list! It would be possible to do a lengthy post on each of those questions, but I'll try to keep this from being interminable.
First a caveat. There's an enormous amount of information out there about sailing ship modeling, the Constitution, and sailing warships in general. For newcomers it has the potential to be really intimidating and downright discouraging. Nobody in this Forum - least of all me - wants to have that effect on anybody else. I'm sure you'd make the same observation to any newcomer in the aircraft realm. Don't feel like you're expected to read and absorb everything, or to achieve near-perfection the first time around.
Now, I'll see what I can do with those questions, one at a time.
1. To build a serious scale model of a sailing vessel, you need a good set of plans. Drawings of the Constitution have been published in lots of sources. The most recent, and probably the most accessible, is the book Anatomy of the Ship: The 44-Gun Frigate Consitution, Old Ironsides, by Karl Heinz Marquardt. It includes more than 250 drawings - not only of the hull and decks but of virtually every individual component of the ship. Marquardt uses the term "gun deck" for the deck in question; "main deck" and "gun deck" seem to have been used almost interchangeably on contemporary plans of frigates. (The uppermost deck - the only one in the Revell kit - is the spar deck.)
That book has generated some rather emotional controversy. If you're interested, check out this thread: http://www.finescale.com/FSM/CS/forums/634200/ShowPost.aspx . I'll stick with the view I expressed there: the author of the book missed some sources that he really should have consulted, and there are some mistakes in it - which are clearly identified in that thread. But it's basically sound, and the illustrations are excellent. For the purpose of building a 1/192 plastic model it's more than satisfactory.
If you're interested in the history of the ship, the first book to get is A Most Fortunate Ship, by Capt. Tyrone G. Martin (USN, Ret.). Captain Martin was the ship's commanding officer during her major restoration for the U.S. bicentennial, in the 1970s. He knows more about her than anybody else; the book is fascinating. If possible, get the revised second edition.
2. I imagine the "brown" referred to in the instructions is mainly on details, such as fiferails and gun carriages. I don't recommend a spray can for any work of that sort. You're obviously acquainted with the range of paints for aircraft models; take a look at the range of browns available from Testor's and PollyScale. Forget the labels; you don't care if it's Israeli Armor Red-Brown or British Dark Earth (or Boxcar Red or Union Pacific Yellow). Look for a few shades of brown that look like wood. Trust your eye. For the exterior of the hull, you're representing the appearance of black paint. Do it the way you'd do it on an airplane.
3. The paint on the real ship during the 1830s probably was glossy or semi-glossy when fresh. There's a general consensus among scale ship modelers, though, that - especially on small scales like this - glossy paint wrecks the scale effect. Most experienced modelers use flat paints, or perhaps paint with just a tiny bit of sheen. I think I'm fairly safe in asserting that, though there are plenty of exceptions, most sailing ship modelers don't use spray paints or airbrushes. Brush painting is a near-essential skill for this kind of modeling - especially on small scales.
4. I think the box art Revell is currently using for this kit was originally painted for the company's big 1/96 kit, which represents the ship's 1814 configuration. The transom in your kit matches the one on the real ship as she was in 1956 - and probably is about right for the 1830s. (Nobody's exactly sure what her transom looked like throughout her history. Marquardt's book shows four versions of it - with three, four, six and eight windows.)
Unfortunately, scarcely any aftermarket photo-etched parts for sailing ship models are available. I am unaware of any aftermarket merchandise designed specifically for a plastic sailing ship kit. Plastic sailing ship modelers do make lots of use of aftermarket cast metal and wood parts from companies like Bluejacket (www.bluejacketinc.com) and Model Expo (www.modelexpoonline.com). But you're not going to find anything like the sorts of "ship sets" that cater to the twentieth-century warship modelers.
5. Yes - it's wrong. Each mast is made up of three parts: lower mast, topmast, and topgallant mast. Each has four yards (the horizontal spars from which the sails are suspended): lower, topsail, topgallant, and royal. (The lower yard on the mizzen mast is actually called the crossjack, or crojack, yard.) The lower yards are fixed in position vertically (though they swing horizontally to let the sails catch the wind). The topsail, topgallant, and royal yards slide up and down when the sails are set and furled. The sections of the masts on which the yard slides can't be painted; the mechanism that lets the yard slide (called a parrel, or parral) would scrape the paint off. The unpainted sections are slushed down periodically with grease, making them a dull, orange-ish brown. The lower masts probably were painted white in the 1830s (though there's some controversy over what colors they were during other periods). The tops, crosstrees, and doublings (the portions where the sections of the mast overlap) were also white. A glance at a good photo of the real ship will clarify all this.
6. If you do a search on the word "Constitution" in this forum you'll find quite a bit of useful information. The ship herself has a website: www.ussconstitution.navy.mil . The Constitution Museum, which is a few yards away from the ship in the Boston Navy Yard, has its own site: www.ussconstitutionmuseum.org . Another very useful site, which one probably wouldn't think of (unless one did a Google search) is www.polkcounty.org/timonier . Polk County, North Carolina, is the current residence of the aforementioned Captain Martin. He's posted some extremely interesting information about the ship on that site - including some material you won't find elsewhere.
Hope all that helps a little. Good luck.