There are lots of good references on the Wasa. The latest and best in print is Wasa I, by Fred Hocker. It’s the first of four volumes that will cover the whole story of the ship, her career, her exhumation, and her conservation in extreme detail. There are two problems with it from the modeler’s standpoint. One - only the first volume is available so far. It contains several fold-out plans, but not a full set. (I assume more plans will appear in the subsequent volumes.) Two - it’s expensive. (I bought mine with Christmas money - good timing.) If you’re really interested in that ship, though, the book is an essential. Here’s a link: http://search.barnesandnoble.com/booksearch/isbnInquiry.asp?z=y&EAN=9789197465908&itm=2
The ship herself also has an excellent website: http://www.vasamuseet.se/Vasamuseet/Vasamuseet.aspx?path=%2Fhome%2Fvasamuseet%2Fom&layout={C0D465E0-3110-436A-A0E4-EA5BB84475B8}
That may furnish all the information you need for your particular project.
The Airfix Wasa kit, incidentally, is one of the best styrene sailing ship kits ever. It’s on a pretty small scale, but an excellent basis for a scale model - if you can live with the “dummy” lower deck guns.
The terms “quarterdeck,” “halfdeck,” and “poopdeck” seem to have been used extremely casually in the sixteenth and seventeenth centuries. So the phrase “turn the halfdeck into a quarterdeck” doesn’t really make much sense. There are so few reliable documents and graphic representations that it’s hard to say what’s authentic and what isn’t. As I remember, the Mayflower II (the 1950s full-size replica, on which the Revell kits are based) has two full-length decks, a raised forecastle deck, a quarterdeck (if that’s what you want to call it) that stretches from just abaft the mainmast to the stern, and a poop deck at the extreme stern. What I’ve just called the quarterdeck is, I think, divided by a low step (less than a foot high) about halfway back. (I’m honestly not sure why, but that configuration does seem to have been common - then and later.) In that case, the section of deck aft of the step is sometimes called the “halfdeck.” But the use of terminology seems to have been inconsistent.
The Mayflower II was designed by William Baker, longtime professor of naval architecture at MIT and a fine scholar. He would be the first to tell you, though, that any reconstruction of the Mayflower - or any other seventeenth-century vessel, except the Wasa - is by definition highly speculative. The hard information about the Mayflower consists of two pieces of data: she was of 180 tons burthen (a figure that’s subject to interpretation), and she had at least one topsail. (John Winthrop’s journal tells about a sailor who fell overboard and saved himself by grabbing “the topsail halyard,” which was dragging in the water.) Beyond that - nobody really knows.
All your ideas sound good - though that’s a lot of work to put into a model destined for the wargaming table! Replacing plastic belaying pins is always a good idea. You might find brass ones preferable to wood ones, though; much more durable, and the brass belaying pins available from the aftermarket companies are far better proportioned than the wood ones.
Good luck.