I'm not a Civil War expert by any stretch of the imagination, but I've had to dip my toe in these rather murky waters a couple of times. Quite a few years ago I got hired to design a paper model (for kids) of the Monitor, for use by the Monitor Marine Sanctuary's educational programs. And just a couple of years ago my students and I did a class project around the remains of the C.S.S. Neuse, which resides about 25 miles away from her, in Kinston, North Carolina.
The best source on Union ironclads is Donald Canney's The Old Steam Navy:Vol. II, The Ironclads, 1842-1885. I don't have the book, and it apparently is out of print, but it's the sort of thing a good library would have - and I'm sure used copies can be found. Don Canney is a fine scholar and the book is well-illustrated. I'm not sure how many actual plans are in it, but my guess is that Don found whatever was extant.
The accepted authoritative source on the Confederate ironclads still seems to be Iron Afloat: The Story of the Confederate Armorclads, by my former colleague William N. Still. That one is in print; here's a link: http://search.barnesandnoble.com/booksearch/isbnInquiry.asp?z=y&EAN=9780872496163&itm=1
There are quite a few good books about Civil War weapons. For naval guns, the one I'd start with is Spencer Tucker's Arming the Fleet: U.S. Navy Ordnance in the Muzzle-Loading Era. That one, unfortunately, is also out of print.
Many years ago a gentleman named Earl Geohagen drew a series of plans covering most ships that served on both sides of the American Civil War. He knew his stuff, and covered the bases pretty well regarding sources. His drawings have been around for a long time, and some additional material has surfaced since he drew them, but they're a good start. The originals are now in the Smithsonian; I imagine copies are available for sale there.
The consensus among the researchers who've investigated the Monitor seems to be that she was painted black above the waterline and anti-fouling red below - the red being a rather bright, oxide shade rather than the dull red we associate with hull bottoms today. The Neuse's remains are in bad shape; she's had a rough life since 1865 - including being scuttled, excavated by amateur archaeologists who cut her in half, and walloped by two major hurricanes. (Better days for her are on the horizon; that's another story.) There's no hint of any paint on what's left of her. The dedicated (nay, obsessed) guys responsible for taking care of her think, on the basis of photographs of similar ships (e.g., the Albemarle, which was also built in North Carolina and was quite similar), that her hull was coated with a concoction containing tar, lampblack, and (maybe) black paint, which, if it wasn't pure black, must have been close. (The same substance seems to have been in widespread use in the Confederate Army as a protective coating on such things as cannon barrels.) The Neuse folks think it probably was applied (likely with mops) to all the above-water exterior surfaces - including the unarmored deck planking. Not exactly an inspiring color scheme.
Figuring out the colors of such ships on the basis of black-and-white photos is, of course, tricky. The ships sometimes look grey, but the angle of the light striking an object that's painted black can be deceptive. Some, at least, of the Confederate ironclads operating on the Mississippi River certainly look in photos like they're a rathe pale grey.
I hadn't heard about Confederate ironclads being painted with red oxide, but it's certainly believable. And I personally wouldn't rule out the possibility of unpainted ironclads. The image of shabby, rusty Confederate equipment often gets exaggerated, but it certainly is true that the Confederate Navy constantly had supply problems. And I suspect rust was not a particularly big concern for those people, especially late in the war.
That's about all I can offer. Maybe there are some more knowledgeable Civil War fans among the Forum membership who can help more.
Later edit: It looks like Steves and I were typing at the same time. I haven't dealt with the source he cited, but I've heard of it; I'm sure it's a good one. I wonder if some of those plans listed as being from the National Archives are in fact Mr. Geohagen's drawings.