Well, Tilley's right here - but can't help a great deal. The literature of the period (and after, by the historical novelists) is fond of describing "snow-white decks" produced by holystoning. Logic suggests that this is an exaggeration, but the weather decks of the period almost certainly were, with rare exceptions, bare, unpainted wood. (I believe - though I'd be lying if I said I was certain - that the red paint custom was confined to such spaces as the orlop and sick bay. And recent research suggests that the red paint was simply a primer/preservative; any effect of camouflaging blood probably was incidental.) The color probably was fairly similar to that of the unpainted decks one sees today.
In the old days of PolyS paint, I was fond of a color called "Sahara Sand" for decks. It was essentially a dull grey with a beige tinge. The newer PolyScale railroad color called "Weathered Concrete" comes close.
One of my few complaints about the movie "Master and Commander" was that the ship's decks were too dark. Looked like they might have been made of modern pressure-treated pine.
Regarding mast colors, the information is even more scanty. About the only thing that's fairly certain is that they weren't white. That color seems to have been quite rare in ships prior to about the second quarter of the nineteenth century. My best suggestion is to take a careful look at the various paintings and lithographs of the battle between the Chesapeake and the Shannon. Pay careful attention to the dates at which the artwork was created; don't be misled by some 20th century artist who may or may not have known what he was doing. Find the oldest rendition available and extract every crumb of information from it that you can.
The Chesapeake is a good - and grievously neglected - model subject. The only Chesapeake kit I've ever encountered is a tiny 1/700 cast metal version by the British firm Skytrex. I haven't seen that kit, but if the firm's H.M.S. Victory is any indication, its products are excellent.
Good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.