Well, let's take up the questions one-by-one (realizing that any answers I give are nothing but personal opinions).
There are lots of ways to deal with ejection pin marks - and they can indeed present a problem especially on a kit that came from 1959 molds, as the Revell Cutty Sark did. Which approach is appropriate depends on the individual situation. Sometimes it's possible to sand a relatively large area surrounding the mark, without destroying any detail. Sometimes you can get away with scraping the surrounding are (consider using a small chisel, or maybe an x-acto blade ground down to a custom shape.) Sometimes there's no solution other than filling the depressed area. In that case, I find the best filler is slow-setting CA adhesive (aka superglue), with help from a drop of "activator" or "accelerator" (two names for the same stuff). Put a little of the adhesive in the middle of the ejector pin mark. If it doesn't dry right away, add a drop of accelarator. Then scrape, sand, or file the resulting projection flush.
Regarding the deck - first, are you sure you meant to type the word "boxwood," rather than "basswood"? (Boxwood is an extremely hard, dense, yellow carving wood that's hard to find and quite expensive. Boxwood is much softer, and is sold in most good hobby shops.) In either case, in order to offer a suggestion about the sequence of assembling the hull and the deck I'd need to know just how much you've done already. The main and poop decks of the Revell 1/96 Cutty Sark consist of three parts, with butt joints between them; the difficulty of eradicating those joints has been a plague on people who've built that kit for fifty years now. (Geez - this is the 50th anniversary of that kit's initial release! I feel old.) Applying wood planks over the plastic deck parts is an excellent way to get rid of the joint problem. I hope you didn't glue the three deck sections together and plank them without mounting them in the hull first. (If you did, you're liable to get a nasty surprise when you try to mount the deck to the hull. The deck has to assume a gentle vertical curve, which it's forced into by the gadgets that are molded into the insides of the hull halves. If you've planked the deck outside the hull, the action of bending it to match the ship's sheer is likely to break some of the planks loose.) I would strongly recommend planking the deck after the deck is attached to the hull - and I guess that pretty much answers the question. If you have in fact planked the whole maindeck before installing it in the hull, my suggestion is to install it in the hull now. There may indeed be a problem with the deck parts twisting as they're installed, but I'd be more worried about what's going to happen when they get forced to match the sheer of the hull. The deckhouses, deck furniture, and fittings aren't really difficult to install after the deck is mounted to the hull.
One job that I would recommend tackling before installing the deck: paint the interior of the bulwarks and the waterways (the edges of the decks that are molded integrally with the hull halves). The interior of the bulwarks is white, up to the level of the main rail. (They are in reality made of sheet iron.) The uppermost sections of the bulwarks are made of wood - varnished on the inside and painted black on the outside. The waterways are iron. The teak deck planking is laid on top of the waterways; if you used 1/32" thick planks, they'll stick up just about the right amount. After the planks were installed the waterways were filled with cement, which was scraped to a sort of dish-shaped cross-section. I wouldn't worry about that detail on the model, but I would suggest painting the waterways in the prototype color, which, surprisingly, is a rather bright red. (At least it was the last time I saw the ship. It's entirely possible that the research in conjunction with the current restoration has revealed something different. There may be something about it on the ship's website.)
That's about the best I can offer on the basis of what you mentioned. Good luck.