I'm not sure I quite understand the problem. (Does "at least 1/200 scale," mean as large as 1/200 or as small as 1/200? For that particular ship, 1/200 scale is pretty small. Verlinden, incidentally, makes a resin Monitor kit on that scale; it certainly appears to be a good, accurate product: http://www.squadron.com/NoStock.asp?item=VE2078 )
In any case, the Monitor is a reasonably well-documented subject - with some frustrating exceptions. A great deal of research has been done on the wreck, and the pieces (most spectacularly the turret) that have been brought up. The big problem has always been that, since the ship landed on the bottom upside down, various features on top have not been visible. I have the impression that what's left on the bottom now has pretty thoroughly disintegrated; I don't think there's much hope of finding the pilothouse. (If any of it still is intact, it obviously is the modified version, with sloping sides, that was installed after the battle with the Virginia.)
I had to do some digging about this subject quite a few years ago, when I got hired by the Monitor Marine Sanctuary to design a paper model of the ship. (The model was intended primarily for kids, but the Sanctuary folks wanted it to be right.) I was advised to follow two sets of plans. One was the beautiful set of hand-drawn and color-tinted ones, on one sheet of drafting cloth, supposedly drawn by John Ericsson himself. At that time it was in the collection of the American-Swedish Historical Society in Philadelphia. (I haven't studied this matter in about 25 years, but I imagine it's still there. The Society was quite protective of it - for good reason.) An engraving based on that set of drawings was published in 1862. It's been reproduced in various books, and on the web:
http://www.history.navy.mil/photos/sh-usn/usnsh-m/monitr-v.htm
The other source the Monitor Sanctuary folks told me to use was the book U.S.S. Monitor: The Ship That Launched a Modern Navy, by Edward M. Miller. It contains a modern (i.e., 1960s or 1970s) set of drawings by Alan B. Chesley. The word I got from John Broadwater, who was in charge of several diving expeditions that went down to the wreck, was that the Chesely drawings were as reliable as anything else in print at that time. The book unfortunately is out of print, but several used copies are available (at pretty reasonable prices) via the Barnes and Noble website:
http://search.barnesandnoble.com/booksearch/results.asp?WRD=U%2ES%2ES%2E+Monitor%3A+The+Ship+That+Launched+a+Modern+Navy&z=y
It should be fairly easy to take the dimensions of the pilothouse off either of those drawings.
My familiarity with this stuff is pretty seriously out of date, though. The exploration of the wreck and the raising of the turret have led to some rethinking of just what the ship looked like. For a long time, for instance, nobody was quite sure what the top of the turret looked like. (Metal grating? Wood grating? Solid iron plating? The alleged Ericsson drawing doesn't make it clear, and the top of the turret wasn't visible until the whole thing was brought up.) If you do a search on the word "Monitor" here in the Forum, you'll find some interesting discussions. Here's one such link:
/forums/1/598128/ShowPost.aspx#598128
I suspect some more revelations about this important ship in the next few years, as the conservators continue the long, precise job of cleaning up the turret and other components that have been raised. A new book, containing a new, detailed set of plans, probably will appear before too long. In the mean time, though, so far as I know the Ericsson and Chesley drawings are the best graphic sources.
I suspect Mr. Williams already knew all that - but if not, maybe it will help at least a little. Good luck.