Don: I'm not familiar with the markings you describe. They may represent an attempt to mark ownership (similar to an owner ID today), possibly a livery. I've seen hulls marked under the canvas by people who have restored a given canoe, but nothing under the deck. Other members may chime in with their experiences.
Restoration latitude runs the full gamut, from people who want the canoe to be better than when it was new using only the original species, to people who are looking for a functional restoration to get the boat back on the water. My opinion, unless the canoe has significant historic or personal value I try to match the original but if the material is not available I'll use something else. Old Town produced 3 grades of canoes (AA, common sense and guide) and used mahogany for their AA grade boats. Probably only our group would realize that you replaced the spruce gunwales with mahogany on a CS grade boat. It goes back to your preference original vs functional.
Do not hesitate to ask your restoration questions here. This is what the forum is for. Try the search function first, many times a problem that seems unique to you may have been asked before. If not, ask away, one of the special characteristics of this membership is the willingness of our members to share their talent and experiences. It is not unusual for some of the best known restorers/builders to reply with in depth explanations as to how to resolve your given problem or answer your particular question. Everyone is in it for the same reason to promote our passion of w/c and birch bark canoes.
Welcome aboard,
Al