As usual in any Santa Maria project, we know so little about the real thing that it's impossible to give definitive answers. My guess is that the Spanish shipbuilders made masts and yards out of single trees whenever they could - and in those days big trees were much more common than they are now. I have a vague recollection that the old Revell Santa Maria depicted the main yard as being made from two pieces of wood overlapping and lashed together in the middle, but I have no idea how Heller handled it.
I also don't know what sort of finish or preservatives the Spanish may have used at that time. In later periods there are references to "blackening the yards" - probably with some substance containing tar and/or lampblack. But what, if anything, was used for that purpose in 1492 is anybody's guess.
You've had impressive success at giving the "wood grain" impression on the hull. Something similar would be appropriate for the masts and yards. Here's a trick you might try. Start by painting the entire spar with a good, even coat of beige or light brown. Let that dry thoroughly. Then take a bottle of dark brown and dig a dollup of thick, gooey pigment out of the bottom. Put a good-sized drop of that substance on one end of the spar and let it dry for a minute or so. Then sploosh one of your fingers in it and run the finger down the length of the spar, leaving a fairly straight but irregular pattern of the dark brown behind. With a little practice you can do a remarkably convincing immitation of wood grain that way.
The Pamir, of course, is another story entirely. Most of her spars were made out of steel, and painted.
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