I want to start work on my Monitor & Virginia iron clad ships. What would be the most appropriate color for the ships? Bare Iron would have rusted very quickly and the two would have been rust brown. Were the plates and decks painted? What colors?

What would have been removed going into combat? the Virginia's boats would have been stowed or left behind. Monitor's canvas turret cover taken off.

I'm going to say mostly black. See this painting.
http://en.wikipedia.org/wiki/File:The_Monitor_and_Merrimac.jpg

Also, the Mariner's Museum, in VA has a mock-up. Black above the waterline and red below.

You might also read through this

One thing I have learned during my research is that the CSS Virginia had its iron plates coated in "Tallow" to hake the shots slid off. Tallow is rendered fat, so the finish on the iron plates would have been shiny.

The USS Monitor had just arrived from open ocean voyage from New York, so I am going to go with some corrosion and rust, since the crew would not of had the time to "clean-up" the vessel before going into action.

You may want to check out the "shiny" rendered fat. When fat gets cool and solidifies, it is not real shiny.

I would think that gunmetal would be appropriate with some flat black washes...

I did an experiment with bacon grease on a steel plate. In October in Pennsylvania it was hazy, until the sun was up for a wile then it was shiny. My experience in Ft Eustis, VA, near Hampton Roads it would be a little warmer, so I will go with a shiny iron look on the Virginia.