I assume vonBerlichingen simply meant "prototype deck" to refer to the deck of the real ship.
As for references, in dealing with this ship you can't do better than the two by George Campbell: his plans of the Cutty Sark, which I've praised many times in this Forum, and his book, China Tea Clippers. The latter has a whole chapter on the principles of deck planking. As of a few months ago, the entire book was available on the web. I can't remember the address; can somebody help?
The planking of a deck on a ship like that is more complicated than it looks at first glance. There are rules governing the disposition of the butt joints, and where the ship's shape tapers fore and aft the planks are not cut off to sharp points. (That's a no-no in shipbuilding.) They're "joggled" into the "margin plank." Mr. Campbell's drawings and text clarify all that. And, as I mentioned in an earlier post in this thread, the planks on the poop deck and the roof of the poop deckhouse are tapered as they go aft. If this is your first attempt at laying planks, I don't recommend worrying about that sort of detail. If you get a nice, even, tight-looking deck you'll be doing fine.
In the case of a model this big, it's probably preferable to install the planking after the plastic deck components have been installed in the hull. As I think I mentioned earlier in another thread, the design of the kit works in your favor a bit. The waterways - the horizontal "edges" of the deck that are molded integrally with the hull halves - are in fact sheet iron. They form a "trough" around the edge of the deck - and if you glue 1/32" planks on top of the plastic deck, the trough will look just about right. (The trough is filled with concrete, which, on at least one occasion when I visited the ship, was painted red.)
You need a flat surface to lay the planks on. Anything that projects above from the plastic deck components has to go - with the possible exceptions of things like the hatch coamings, which you can work around. (I seem to recall that the hatch coamings on the Revell kit are rather heavy, as though they were made of wood. If that's the case, it's wrong. They're made of iron plate.)
About the only practical way to plank a deck is to start on the centerline. Mark the centerline as accurately as you can and lay a row of planks on each side of it. (No plank down the middle.) Let the glue dry thoroughly before you lay the next strake. If you shove each strake firmly up against its neighbor, the lines of the planks should be nice and straight when you're finished.
Before you lay each plank on the main and forecastle decks, run a medium-hard pencil around all four of its edges. The graphite in the pencil will do a beautiful job of representing the caulking between the planks - and it will survive any sanding or other brutalization you inflict on the surface. The planking on the roof of the poop deckhouse is white. I've never tried to reproduce that effect, but I suspect extremely thin white plastic strips laid vertically between the planks would do the job if you want to try it.
Don't waste your time trying to imitate nailheads in the planks. The real things are held down by iron bolts in counterbored holes, with wood bungs covering the heads. In 1/96 scale they'd be virtually invisible.
Hope that helps a little. Good luck.