The question of gauge has been pretty well covered by previous responders.
One more book to suggest:
Civil War Railroads and Models by Edwin P. Alexander. It was originally published in 1977 and has been republished at least a couple of times since. Alexander was a well known model railroader during the 30's, 40's and 50's. He wrote many articles for Model Railroader and similar magazines in those days and was a leading light in the NMRA.
The book features 280 B&W illustrations including Civil War era photos and lithos of locos, rolling stock, structures and ROW, along with excellent scale drawings and suggestions for building a Civil War era model railroad. The text is not an in-depth scholarly treatment but certainly provides a good overview of the subject.
I own the Fairfax Press edition published in 1988. A copy of this edition is currently listed on ebay, if you are interested, which you probably will be when I tell that the author's full name is Edwin Porter Alexander and he was the grandson of Lee's famous chief-of-artillery
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