I don't claim any real expertise on this subject, but I have read a little about it. I have the impression that the documentation about color schemes of Civil War vessels is, in general, pretty vague. The written documents rarely mention colors, so researchers are left with two types of sources: contemporary oil paintings and photographs (all of the latter, of course, being in black and white). The photos that exist (and there aren't a lot of them) seem to suggest that most of these ships were painted a very dark color - if not black, then mighty close to it. I think I've seen some reputable models of Confederate ironclads with grey hulls, but I can't recall seeing a model, painting, or photo of a Union turret ironclad that wasn't black.
Some years ago I got hired by the Monitor Marine Sanctuary to design a paper model of the Monitor for distribution to kids. I had quite a few conversations with the historians and underwater archeologists who had studied that ship intensively. They were pretty firmly of the opinion that she was painted black above the waterline and red below - the red being a rather bright shade of red lead primer.
That's about all I can offer. Maybe some Civil War experts out there can contribute something in greater detail.
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