First of all (though I suspect this may incite some disagreement from other Forum members), I really question whether it's necessary or appropriate to replace all those plastic spars. I've never built the Heller Santa Maria, but I've built several from the very similar Revell kit - the first one when I was about six years old. I never replaced any of the spars, and never came close to breaking any of them. I suspect that styrene main lower mast, at least, is plenty sturdy.
Remember that the whole purpose of standing rigging is to support the masts. The old boys who figured out how to rig real ships knew what they were doing. If the stays and shrouds are set up properly they counteract each other's tendency to pull the masts out of line. When you rig the shrouds, for example, the mast may lean back a little, or you may find it hard to get all the shrouds tight. But as soon as you rig the stay, everything will be fine. The running rigging does the same thing for the yards. You'll learn pretty quickly just about how much the mast ought to lean back in order for the stay to straighten it out again. That's part of the skill of rigging - whatever the spars are made of.
Making a spar out of wood is no guarantee whatever against bending or breakage. I don't know what wood dowels are made out of in Taiwan, but in the U.S. they're usually birch. A birch spar with a diameter of less than 1/16" is, if anything, a little more flexible than a plastic one of the same size. (That, admittedly, depends to a large extent on the particular styrne the manufacturer used. Styrene varies quite a bit in terms of flexibility.)
When I was a kid I built dozens of plastic sailing ship kits and never replaced any of the spars. (I'm sure the finished models were, by adult standards, pretty hideous, but for plenty of reasons other than that one.) The last model I built from a kit, the Bounty, has wood spars - but my reason for replacing the plastic ones was that they weren't accurate.
If you do want to make wood spars, and you don't have any references, the best advice I can offer is to make them look as much like the kit parts as you can. I have no idea whether a fifteenth-century nao would have square mastheads - and I question whether anybody else knows for sure. The Heller designers may have made some mistakes in the kit parts, but if I were you I'd hesitate in trying to outsmart those folks - especially in the absence of any reference material.
I'm a little confused by the reference to pendants. In the seventeenth century lines with that name (sometimes called burton pendants) were sometimes rigged permanently on the lower masts of big ships. They were part of the gear for tightening the shrouds. I've never seen any reference to such lines prior to the sixteenth century, at the earliest.
The board sticking out horizontally from the side of the ship is called (in English) a "channel." That's thought to be a corruption of the original "chain wale." (A wale is an unusually heavy timber comprising part of the side of the hull.) The purpose of the channel is to give the shrouds a little additional mechanical advantage by spreading their lower ends apart a bit further, and to keep them from chafing on the rail or other hull projections. Just how the system of fastening the lower ends of the shrouds evolved is a matter of some debate, but a likely explanation is that the deadeye originally was connected to the hull by a piece of fairly heavy chain. The uppermost link of the chain would be connected to the iron strap of the deadeye. (The strop would start out as a circular ring, and be pinched into a shape like a distorted figure 8, with a large loop enclosing the deadeye and a smaller one engaging the link of the chain.) The lower end of the chain would be stapled or otherwise fastened to the hull a few feet below the channel. The edge of the channel would have a series of notches cut it it to receive the strops of the deadeyes. (The deadeye would go above the channel; the small part of the strop, with the chain hooked into it, below.) I don't know just how it was done in 1492, but in later periods a wood molding would be nailed on the edge of the channel to make sure the deadeye strops stayed in place.
By the late sixteenth century that system started to get simplified. Brian Lavery, designer of the replica ship Susan Constant, thinks a medium-sized merchantman of that time (1607) would have "chain plates" in the form of simple iron bars. The lower end has an eye forged into it for a spike holding it to the hull, and the upper end is flattened, bent over into a hook, and hooked into the deadeye strop. In later centuries the chain evolved into two or three elongated iron links, forged individually to fit the ship. By the mid-nineteenth century it had, in many ships, become a single iron bar.
What Heller has done, apparently, is to omit the deadeye and use a single piece of thread to represent the shroud and the chain. The holes in the channels apparently represent the notches in the edge, with the edge molding formed integrally with the channel. Rather than fussing over the fastening of the chains to the hull, Heller is telling you to run the lines through holes in it (and, I assume, secure them inside).
A good, fairly easy method of faking the real thing on this scale might be to get hold of some fine-link chain (either from a hobby shop, a mail order supplier, or a cheap jewelry dealer). Run a piece of black thread around the deadeye to represent the strop. Pass both ends of the thread through the hole in the channel and tie them to the upper link of the chain. Reinforce the knot with adhesive (this is a good job for superglue), and trim the ends of the thread off. Cut the chain to length. Then take a piece of copper or brass wire,double it over, run it through the bottom link of the chain, and shove both ends of the wire through the appropriate hole in the hull. Inside the hull (I assume you still have access to the inside), spread the ends of the wire apart and secure them to the inside of the hull with superglue or epoxy. (There are other ways to fasten the chains to the hull, but this one makes it easy to get the chains nice and tight.) Now your deadeyes are securely fastened to the hull and ready to take the lanyards and shrouds when the time comes.
All this is far simpler in reality than it sounds. Describing the rigging of a ship without pictures isn't easy. You really need some sort of reference book to help with the rigging of this model. Have you tried the local bookstores, or is there a public library nearby? Or a college or university library? It would be a shame to put a great deal of time and effort into the rigging and find out when your books arrive that you've made some major - and easily avoidable - mistake.
Good luck.