I'll take the liberty of offering a couple of small suggestions based on bitter experience.
Eventually you're almost certainly going to want to fasten the model down permanently to some sort of base. There are lots of ways to do that - pedestals, cradles, keel blocks, etc. - but all of them entail mounting some sort of fastenings (probably wood screws) in the bottom of the hull. A permanent mounting system is especially important if you're going to put the finished model in a case - as I hope you are.
Whatever mounting method you use, the sooner you figure it out and make provision for the fastenings, the better. If, for example, you intend to mount the model on a pair of those nice Model Shipways brass pedestals, you'll eventually have to drill a pair of holes through the keel and into the hull. It's far, far easier to do that before you install the bulwarks, deck furniture, etc., while you can still lay the hull upside down on your workbench without damaging something. (Obviously the best tool for the job is a drill press, but it's not essential.) A good way to do it is to make up a couple of simple wood blocks to substitute temporarily for the pedestals themselves while the model is still under construction, and install the real pedestals at the last minute. Then screw the model down to a conveniently-sized board or sheet of plywood. It's not a bad idea to put a couple of additional blocks, with some sort of cloth padding on top of them, so that if you have to exert any forces that tend to twist the hull the mounting screws won't have to take all the strain.
In any case, having the hull screwed down firmly to a board will make your life a great deal easier. As you get further along with the detailing process, you don't want to have to hold the hull in your hands. A further small sophistication is to fasten a couple of strips of wood underneath the temporary baseboard that can be clamped in your vise, to hold the model rigid on your bench.
The idea of gluing a tracing of the transom onto the hull as a shaping guide is sound up to a point - but be careful. (This is going to be a little tough to verbalize, but if you visualize the situation it's pretty simple.) Remember that the side, bow, and stern views on the plans are drawn as though the shapes in question were projected onto a vertical plane. (Occasionally a draftsman will provide an additional "expanded" view of a part like a transom, but that's highly unusual.) The transom is not a flat, vertical piece; it's slanted, and it curves slightly outward in the center. So the view of it from the stern (which shows what it would look like if its outline were projected onto a vertical plane) is different from what the transom would look like if it were (hypothetically) removed from the ship and flattened out. That flattened-out shape is, in essence, what you're going to have to make when you cut a piece of wood to form the transom. If you trace the outline of the transom from the stern view onto a piece of wood (or styrene, or cardstock, or whatever) and wrap it around the curvature of the ship's stern, your transom will be too narrow (because you didn't allow for the curvature) and too short vertically (because you didn't allow for the fact that the transom is tilted). That "projection" phenomenon will also affect the details on the transom. The windows won't be tall enough, and - if the draftsman who drew the plans was really careful - the difference in width between the center window and the ones on the sides will be exaggerated.
I'm not sure how big the discrepancies are; I'd have to look at the plans to tell. I remember when I was working on my little Revolutionary War frigate I plotted out the difference between (a) the vertical height of the transom, as taken from the scrap view in the Admiralty draft, and (b) the actual, linear distance from the top of the transom to the bottom of it, as measured on the sheer plan. The difference was, if I remember correctly, somewhere in the neighborhood of 1/8". On 1/128 scale, that's quite a bit.
There are two ways to solve this problem. The more accurate and meticulous is to make a "true-view" drawing of the transom, plotting out its dimensions from the sheer, body, and deck plans. That isn't as difficult as it sounds, but it does require some careful drawing and a little plane geometry. The other approach is to "eyeball it." Take the actual measurement from the top of the transom to the bottom from the sheer plan (side view). Take the measurement of its width from the body plan (stern view) and add, say, 1/4" to compensate for the curvature. That's too much. So after the transom is in place, trim the ends of it down till they look right. (The first and second Golden Rules of woodworking: #1 - Measure twice, cut once. #2 - It's easier to make a piece of wood smaller than to make it bigger.)
By the way - give careful thought to the material you're going to use for the transom. You can make it from thin sheet basswood; if the model is going to be in natural finish overall that's probably the best route. On my Hancock, whose stern was destined to be painted black and yellow, I eventually decided to make the entire transom assembly from sheet styrene. It's amply flexible to wrap around the curvature of the stern, holds a nice, sharp edge, and can easily be cut to form the window openings. (I made the windows themselves from clear styrene sheet, with the "frames" made from waterslide decal stripes. But I was working on a scale twice as small as the Sultana's. Remember that the window in the center of the transom is a painted dummy; real glass in that location would only serve to give outsiders a view of the rudder. (I know of at least one other famous ship that had a fake window in her transom. An entry in the logbook of H.M.S. Bounty mentions that, one nasty day off Cape Horn, a sea "struck the stern and stove all to pieces between the cabbin windows, where the sham window is.")
Good luck.