Kudos Milton she is a handsome ship if there ever was one.
At the begining of your post you had some questions about what was possible with animations, flight model, etc.
If you are not aware, there are several old (FS 9 or earlier) sailing ships I've downloaded & tried (in FSX).
I suggest you check out the "Bonhomme Richard", Schooners "Pride of Baltimore" and "La Recouvrance", or XIX Century Sailing Frigates from Pierre de Rotalier.
Also the modern yachts by Deltasim Studio (some freeware). I believe I got them from Flightsim.com.
The older ships generally had 4 models - sails up or down, & heeling to port or starbord. You had to change "aircraft" to make them appear in accord with their sailing situation. Otherwise setting/hauling anchor, running the cannon in/out, & hoisting the flag, etc. could be controlled with spoilers, flaps, exits, & landing gear control keys. You also have water rudders available in FSX. Animated flags, that change direction with the wind are cool, & useful when sailing. One model also "fired" the guns with a flash & splash effect, which had to be different if the ship was leaning left or right. This could be toggled with lights (O for Strobe), while I prefer setting them as smoke effects (I key). Nav lights should be appropriate for ships. Some also had bow & stern wake effects. Rising black smoke might be appropriate for simulating dammage.
Regarding the "flight" modeling, they generally bobbed with the waves. Float & thrust positions play a role in this. Try piloting from the helm & observe what you can see over the bow. All were "sailed" with fake prop or jet propulsion (silent engines). Sometimes nautical sounds were substituted - this adds a LOT to the immersive experience.
It would be better to do things like Deltasim, with one model that obeys the laws of physics according to the flight model, inertias, sail area, wind direction & strength, etc. Sail animations can be controlled with flap positions or the spoilers. However, modeling the true behavior of sailing ships is hard to do within the limitations of Flight Sim.
Good luck with your project,
JG