One other possible kit occurs to me: the old Pyro "Brig of War." This was a tiny kit (when I was a kid it sold for 50 cents), based, like so many other Pyro kits, on a Model Shipways wood kit - in this case the brig Fair American, from the American Revolution. The MS kit, in turn, was (and still is; it's just been reissued) based on an old model in the U.S. Naval Academy Museum. Nobody's 100 percent sure what real vessel (if any) the museum model represents (perhaps an American privateer), but it's a fascinating model of an attractive little vessel.
The Pyro kit didn't amount to much; it had only a handful of parts, including injection-molded "sails," and was intended primarily, I suspect, for younger modelers. And it had a pretty clearly 1770s or 1780s look to it - a good bit broader in the beam than would be likely for a vessel of the 1790s. (I think Pyro may in fact have distorted the proportions of the Model Shipways plans a little; my memory's foggy on that point.) But it did have some rather nice little guns - and a raised quarterdeck. (That configuration was fairly common in brigs, schooners, and even single-masted sloops and cutters during the last half of the eighteenth century. The quarterdeck wouldn't interfere with the boom, as long as the quarterdeck didn't project much above the bulwarks.)
I have no idea how hard the Pyro "Brig of War" is to find nowadays. But if you do run across one, and don't want to spend more than a few weekends on a "Jack Aubrey" project, this little kit might be a good starting point. I certainly had a lot of fun with it years ago. A careful paint job and a bit of improvement to some of the deck and hull details, along with some rigging, could turn it into a really pleasant-looking decoration - and on such a tiny model few observers would complain if the rigging was simplified a good deal.
H.M.S. Beagle did indeed start her life as a brig-of-war. She was very heavily modified - almost beyond recognition, in fact - in preparation for the surveying/exploring voyage in which Darwin participated. Her upper deck was removed and rebuilt on a higher level (presumably to make her a bit more habitable for such a long voyage), her armament (or virtually all of it) was removed, and she was given a third, fore-and-aft-rigged mast. That addition made her into a bark (or barque). (A brigantine has two masts - the foremast square-rigged, the mainmast fore-and-aft-rigged.) The new mizzenmast was permanently stepped, and, so far as I know, she kept it for the rest of her days.
The connection between the Beagle and the Bounty is, so far as I can tell, a piece of complete fiction generated by Revell purely for purposes of marketing. The two ships had virtually nothing in common. Reliable contemporary plans of both have survived; they show vessels of completely different proportions, dimensions, and hull lines.
Unfortunately the Revell Beagle/Bounty hoax seems to have been picked up by some other people who should have known better. Mamoli, one of the HECEPOB (Hideously Expensive Continental European Plank On Bulkhead) kit manufacturers, has recyled its Bounty kit into a "Beagle," which sells for several hundred dollars and quite obviously is a copy of the Revell one. (Such fictitious Revell additions as the phony-looking deckhouses, which have no basis in reality, show up again on the Mamoli kit. There's just no way two minds could conceive such nonsense independently.) Somebody in Mamoli's employ drew up a set of "Beagle" plans that obviously are copied from the Revell kit, with some impressive-looking but thoroughly fictitious rigging details added. Those plans, I think, have been reprinted in some other publications, apparently leading quite a few people to think there was some connection between the Beagle and the Bounty. There was in fact none whatsoever.
I wish some manufacturer would release a genuine, scale model of the Beagle. She was an interesting, historically important vessel - and there's more than enough information available to make a nice, accurate model of her. Some years ago Donald McNarry, one of the best ship modelers in the world, did a beautiful small-scale model of her; he wrote an article about the project for the British magazine Model Shipwright. I also have very pleasant memories of a BBC/PBS TV series, called "The Voyage of Charles Darwin," that ran in the late seventies. The acting, narrative, and scenery were first-rate; the ship that represented the Beagle suffered from many of the usual movie-maker's inaccuracies and anachronisms, but looked nice in the distant shots. That series achieved something rather remarkable in my family: my brother, who's a professor of zoology, and I got equally interested in it - and had equally high opinions of it. If it showed up on DVD I'd buy it in a heartbeat.
Sorry for drifting away from Captain Aubrey. Good luck.