I did this to a Revell Constitution many years ago. It worked quite well, and actually was pretty easy - probably not much more difficult or time-consuming than eradicating those awful joints between the plastic deck sections.
My recollection (beware: this was a long time ago) is that both the main deck and the spar deck are supported by hefty pins sticking out from the insides of the hull halves. The pins, I think, are in pairs. On the underside of the deck section, in line with the gaps between these horizontal pins, are a series of vertical pins, each of them mounted on a rectangular pad that (fortunately) is just about 1/32" thick. The pads sit on the pins that project from the hull.
Shave off the pads and the pins from the undersides of the decks, and the decks drop by 1/32". Thank you, Revell. (The Cutty Sark is tougher: no pads.)
I don't recommend either the glued-up decking sheets or the scribed ones. Neither is as effective as individual planks - and for a model this big you'd have to splice the sheets together at the ends anyway. You'd also have to cut extremely precise holes in them to fit around the hatches and other pieces of deck furniture. The easiest way to handle the problem is the best-looking: make the deck from individual planks.
The best wood for the purpose probably is holly, but it's hard to find. Maple is a good second choice, but you'd probably have to mill the planks to size yourself. Decent hobby shops (and mail-order firms that cater to ship and/or railroad modelers) sell strip basswood, which is pretty good stuff if you're careful with it.
I don't remember the width of the actual planks; my guess is about 9", which translates into 3/32" on the scale. The necessary bundle of 3/32" x 22" stripwood will set you back a few sheckles, but I suspect you'll conclude the results are worth it.
You probably already have some books about the laying of prototype deck planking. (If not, do another post and I'll recommend some.) The arrangement of the butt joints is crucial. If you get really ambitious you can have lots of fun reproducing the "joggling" of the margin planks at the bow and the stern. I confess I didn't do that when I built my Constitution, but I'd probably take a shot at it nowadays.
The typical plank is about 24' long - that is, 3" on the scale. I recommend chopping up a considerable number of planks (a Northwest Shortlines "Chopper" is ideal, but any sort of jig that gives a nice, 90-degree cut will do fine), so you can work in batches of a dozen or two.
I've seen lots of tricks for representing the caulking between the planks, but to my eye the most convincing one is the easiest. Before laying each plank, run a fairly soft (say, #2) pencil around all four edges of it. The result will be that each plank is surrounded by a thin, dark grey line that will resist any sanding, scraping, or other brutalization you inflict on the finished deck.
I glued my planks down with old-fashioned, tube-type Revell plastic cement. It worked fine. (That particular model is no more, but I've got a couple of others on which I used that adhesive for wood-to-plastic joints. They've lasted more than 20 years.) Alas, Revell cement seems to be extinct, but I imagine the Testor's variety would work. The idea is that it soaks into the wood a little, and dissolves the surface of the plastic "under-deck."
Once the planks have been prepared, you'll be surprised at how fast the actual laying of them goes. You probably can do the spar deck in two or three hours.
The hatch coamings that are cast in with the plastic decks will now be 1/32" too low. You can fix that by gluing strips of wood on top of them. (Pay some attention to the corners. Miter joints are verboten in traditional wood ship construction. If I remember right, Revell did a nice job of scribing the "ship joints" at the corners of the hatch coamings.)
Initially you may be a little disappointed in the appearance of the result, but have faith. Let the glue dry thoroughly, then work over the deck with extremely fine sandpaper.
To get a good, deck-like color I recommend a thin coat of "Driftwood" wood stain, sold by Olympic Paints. Maybe mix it with a little "Golden Oak." When the stain is dry, give the whole deck a coat of white shellac, dilluted almost beyond recognition with denatured alcohol. Shellac is great stuff for this sort of thing. It settles the slightly fuzzy grain of the basswood, and provides good protection agains future paint dribbles.
I've probably forgotten some aspects of this job, but that's the gist of it. As I recall, the whole process of planking the decks took less than a week of evenings. But it changed the whole character of the model.
Hope all this helps a little. Good luck.