I would not suggest using any "reddish" wood, like mahogany, cherry or any exotic wood which looks nice on models but actually spoil the authenticity of the model.
A small research should be done about build model to find out what kind of wood was used at that time and kind of ships.
You would never mistake using walnut in the first place or oak veneer for the second planking since the most of the sailing ships were build from that wood due to their superb characteristics in the maritime use.
I would prefer walnut veneer planking for San Felipe, stained by some acrylic colorless wood stains no glossy at all if possible. and all painted ornaments and colors on that ship to be slightly blended, paled, not vivid like on the plastic toys. A bit of "patina" over it would make your model just perfect .
Try to avoid any reddish or light colored wood since they have never been used in shipyards from 15th to 19th century (except for expensive captain's cabins furniture).
Finished model should resemble the real ship, not to just serve as a nice toy in the glass display.
If you let me say one more thing- try avoiding any kind of varnish- old sailing ships were never "varnished" they were sealed and impregnated by oils, tar, oil based paints (later). They had their vivid colors only after leaving shipyards. A few months on the sea, the most of the vivid colors got pale and blended. The more realistic colors of the 16th century ships for example, are more like these on this model from my previous build.
