Well, I'll take a shot at the questions in order. Bear in mind that the following are personal opinions. I hope other Forum participants will jump in.
1. The order of assembly is up to you - subject to the limitations of what parts have to be installed before others in order to make sure things fit. My general approach is to assemble as much of the basic "carcass" of the ship as practicable before painting it. Some fittings (e.g., hatch coamings) can best be installed before they're painted. Others (e.g., gun carriages) really need to be painted first. But the sequence is largely up to the modeler.
2. There are lots of ways to make plastic look like wood. To some extent the method to pick depends on how the manufacturer has handled the problem. Some Revell and Heller kits feature "surface detail" that represents (sometimes quite well, sometimes not so convincingly) the grain of the wood. If I remember properly, the Airfix Bounty doesn't have that kind of detail. My approach probably would be to start out with a coat of a relatively light brown, then add some shading and a bit of "wood grain" effect by dry-brushing two or three shades of darker brown. It would be worth the trouble to take a look at some photos other Forum members have posted. There are some good examples of "wood grain" effect here.
The Bounty quite definitely had a copper-sheathed hull. (The documentation establishes that beyond any doubt.) Just what color it would have been is a matter of some debate. Part of the theory behind copper sheathing was that the friction effect of salt water as the ship moved would constantly erode the surface of the copper, leaving the surface bright all the time. I have my doubts about that. When copper is exposed to air for a prolonged period it turns a remarkably light, bluish green. Salt water seems to make it turn a duller, darker, mottled brownish green - though that probably varies with the precise composition of the metal. (Incidentally, what we're talking about in the case of an eighteenth-century ship is indeed copper. In the middle of the nineteenth century copper ["red metal"] started giving way to a brass alloy ["yellow metal"].) After the ship had been in the water for a while the copper undoubtedly would weather in various ways - and various substances, including seaweed and other marine life, probably would stick to it. I'm not sure a genuinely accurate representation of an eighteenth-century ship's bottom would be something I'd want in my living room.
For what it's worth, on my model of the Bounty (which is based on the Revell kit, which doesn't represent the copper sheathing) I used pieces of .001" copper sheet, applied with contact cement. I weathered it with various shades of green, brown, and grey acrylic paint, dry-brushed in vertical strokes. I'm pretty happy with the result. But that's only one approach.
3. I don't know of any serious ship modeler who has any use for the vac-formed "sails" that come with plastic kits. My custom is to throw them in the trash before leaving the hobby shop.
We've had a rather lengthy discussion in the Forum about this topic, in a thread titled "Real cloth sails?" In that thread I made a case for furled sails as a nice way to display a ship model. That's how I rigged my model of the Bounty. I just moved that thread to p. 1; it should appear a few lines below this one.
4. You're right. The exterior hull planking probably was oak, and treated with some sort of oil-based varnish. Some modelers have suggested, in fact, that the substance in question darkened with age, to the point of being almost black. I have my doubts about that. I think a warm, medium brown, about like the color of Bounty III's hull, is about right. The wales - the thick belts of planking just above the waterline - probably would have been "blackened" with a mixture of tar and lampblack.
The deck probably would have been a softer wood - pine or fir. And part of the ship's daily routine was the "holystoning" of the deck. A holystone was a chunk of pumice, which the sailor scraped over the wet deck planking to scour it clean. Deck planking rarely, if ever, had any finish applied to it; the idea was to make it as un-slippery as possible. For a good deck color I like a light grey with just a tint of beige. (The color that forms the background of the page you're looking at right now is, to my eye, just about right - though maybe just a trifle dark. At least that's how it looks on my monitor.)
I'll take the liberty of offering one more suggestion. The first step in building a good scale model of anything is to get a clear idea in one's head of what the real thing looked like. In the case of a sailing ship, that means studying a good set of plans. Photos of the various replica vessels are extremely valuable, but nothing can substitute for good plans. They're particularly crucial when, as in the case of this Airfix kit, the manufacturer has screwed things up. I don't think it would be too difficult, for instance, to fix that ridiculous slope of the deck, with the help of the drawings in Mr. McKay's book. (The lowest point of the deck is supposed to be right around the middle of the ship's length; both the forward and after sections are supposed to sweep gently upward, almost, but not quite, following the sheer of the main rail. Airfix's deck slopes down steadily from the stern to the bow. That's utterly absurd.) And the aforementioned error in the windlass post can be fixed in a few minutes IF you know what it's supposed to look like. I'm not sure how hard the McKay book is to find, or how expensive it is, but if you get a copy of it you'll wonder how you ever thought you could get along without it.
One more. If you don't make any other modifications to the kit, please cut the studdingsail booms off the topgallant yards. Here the Airfix designers demonstrated that they just didn't understand what was going on. The Bounty had studdingsails all right; they're mentioned several times in Bligh's log. But she didn't have royal yards. (Actually she eventually did get one; Bligh concluded that the lower studdingsails were "too long," so he "cut them and made a royal out of the canvas." But that surely was just a small, temporary sail set on the fore- or mainmast.) The purpose of a studdingsail boom is to spread the foot of the studdingsail above it. In the absence of royal studdingsails (which were just about unheard of in the eighteenth century), a studdingsail boom on a topgallant yard makes no sense.
Hope this helps a little. Good luck.