Quite a few years back I got hired by the Monitor Foundation to design a paper model of the ship - suitable for assembly by kids, but as accurate as I could make it within the limitations of a reasonable number of paper parts. (The Monitor makes an excellent subject for a paper model, because her basic shape contains no compound curves.) I got in touch with one of the archaeologists who had dived on her, and read all the published works I could find. (The drawings that got the highest recommendations were the ones made by Allan Chesley for a book entitled, if I remember right, U.S.S. Monitor: The Ship That Launched a Modern Navy.)
The color scheme I was instructed to use was quite simple: above the waterline - black (or mighty close to it). Below the waterline - lead oxide red. In practice I made the hull above the waterline a very dark grey, so the black plating lines, air ports, etc. would be visible. The red below the waterline, as it was explained to me, was a surprisingly bright, slightly orange-ish shade - not the dull red anti-fouling paint we're used to seeing on more modern ships.
This was a long time ago (about 1985, if I remember right). A lot of additional research has taken place since then; I wouldn't be at all surprised if somebody had found out something different about the color scheme. On the other hand, nobody with any credentials has ever told me there's anything wrong with the scheme I used - and I believe the Monitor Center (at the Mariners' Museum) is still selling the little paper model.
Hope that helps a little.
Youth, talent, hard work, and enthusiasm are no match for old age and treachery.