I am doing legal research for a professor at my law school who is creating a database system of all international patenting law and a collection of any patents filed during the modern era. I am working on the Confederate states during the CSA, and am having trouble finding anything beyond the Act pertaining to patents. Does anyone know what happened to patents filed in the southern states during this era, and is there a database?
I actually wrote a paper on Confederate draft resistance while I was in law school, so I ran into some of the same problems you ran into. I'd use "The Patent Office Pony" as my starting point-- just beware that because Richmond was burned in 1865, precious little survives from the Confederate bureaucracy.
http://www.amazon.com/The-Patent-Office-Pony-History/dp/1887901132