The reliability of the accuracy of newspaper and periodical wood block carvings has always been uncertain. It is hoped they were rendered from "at that moment" drawings, but the possibility that some craftsman sitting at a desk in Pittsburgh extrapolated from his experience is very real. Edward McCaul, in his "To Retain Command of the Mississippi," believes the images were drawn by an eyewitness, and accurate.
Even this image
link
is likely inaccurate. Even if a valid image, it appears to reflect a late war, "tinclad," configuration.
My best guess is that the OP image is pretty accurate, tho none of the openings were being used as gunports. This would follow after being taken into Union service.
As completed as a ram, Little Rebel was armed with a single 24pdr smooth bore at her stern. (McCaul) the other rams had 32odr smooth bores at their sterns, and 4 of the were fitted with 8" smoothbores, from the arms at Fort Pillow at their prows.
So, to address the OP question, windows and doors.