Leave the decks as they are already now. They should be yellowish sort of. You will never get that grey colour which comes naturally after contact with water over time. Normally for decks in models white woods are being user i.e. birch, holy, avodire... and others, but we are getting into wooden ship building. You made it with bright plywood. That is fine.
The only thing which is missing to me (sorry to mention) is luck of culking... those black lines between the planks, insulations.
The masts, I would make also from some bright wood. In reality masts were made of pines so yellowish. But pines do not look too good on models, neither oak. On many replicas you will see them quite dark because of treatment and water. Perhaps you can get some nice pieces of walnut or alder. That would give you nice colour. Should they be yellow - go for cedar or avodire.