As I've mentioned in several other threads, the best source of information about this ship is the set of plans (three sheets) by George Campbell. These drawings, and the notes that are plastered all over them, are a wonderful, fascinating source of information that will tell the modeler considerably more than he/she is likely to need in order to build a fine model of the ship. They're also, even with the current unfavorable exchange rate between the dollar and the pound, very reasonably priced - one of the biggest bargains in model building. An additional attraction: if you buy them from the ship's gift shop (http://www.cuttysark.org.uk/index.cfm?fa=contentShop.productList&directoryId=6) the profits will go toward restoring the ship after the tragic recent fire.
I can't lay hands on my copy of those plans at the moment. (My computer room got rearranged recently, due to a change of computers.) My recollection is that the caprail and the main rail (the one at the level of the maindeck) were originally varnished teak, and that the mainrail was painted white at some later date. (I may be wrong about that; the plans are the best source.)
As for the white waterline stripe, Mr. Campbell offers the following in his fine book, China Tea Clippers p. 83): "The thin white ribband just above the copper line which was painted on the Cutty Sark in her retirement was not authentic, for her or any other tea clipper, and was a detraction."
I can't comment intelligently on that "black and tan paint" technique that the instructions recommend for the decks. I imagine it can be made to work, but I've never tried it. My preference is to paint the deck a dull, slightly brownish grey and weather it with washes and/or dry brushing. But there's no one "right" way to do such things; for heaven's sake use whatever technique works best for you.
There are quite a few ways to replicate boat covers. If I were doing it I think I'd first try making them out of the the same material I normally use for furled sails: thin "silkspan" tissue painted with a mixture of PolyScale paint and white glue. I've never tried making boat covers that way, but I don't see any reason why it shouldn't work.
Good luck. It's a nice old kit.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.