The Merrimac/Merrimack/Virginia has always created big problems for modelers, because the available information about her is so scanty. There's a set of plans for the original (Union) design, and a couple of extremely sketchy measured drawings that apparently were made by the Confederate naval constructor early in the process of converting her into an ironclad. But no reliable plans of the finished product - and, so far as anybody's been able to tell, no photographs. A few pieces of her have survived in museums, but whatever was left of the hull (after it was blown up) has never been found. (If any of it exists, it's on Craney Island, which is a naval installation - and the Navy is reluctant to let researchers near it.)
The old Pyro version is indeed pretty awful (though maybe the Monitor that comes in the same box is worse; how on earth could anybody miss the fact that the turret is supposed to be centered on the hull?). The equally ancient Lindberg one isn't much better. (I remember pretty distinctly that Lindberg had its own ironclad pair, back when Lindberg and Pyro were competing with each other. I'm pretty sure the Lindberg Monitor had its turret in the right place - and the Virginia came with an electric motor. There wasn't room for one inside the Monitor.)
I can't pretend to have studied all the available competitors, but I'm aware of three that look reasonable:
Bluejacket: http://www.bluejacketinc.com/kits/cssvirgina.htm ,
Verlinden: http://www.squadron.com/NoStock.asp?item=VE2115 ,
and Thoroughbred Models: http://www.thoroughbredmodels.com/Ironclads.htm .
The Bluejacket one, obviously, is wood, with cast Britannia metal fittings; the Verlinden one is resin, and certainly looks excellent (if I were in the market for such a kit, that's the one I'd probably pick), and only slightly smaller than the Bluejacket one. But it's strictly a waterline model. [I've edited the last sentence; it originally contained some misinformation about the relative sizes of the two kits. Sorry; my fault.] I've got the Thoroughbred one. It's a very nice white-metal casting (with the stack and a few other parts cast separately); it's as well-detailed as could reasonably be expected, but it's obviously quite small.
I'm afraid that doesn't help much. It's a rather unhappy situation. Good luck.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.