I'm not sure that what you are doing is the same as what I had to do, so this may not work for you -
I was once asked to photograph 200+ marked up blue prints about 2' X 3' in size (actually black ink on white paper) with manually marked changes in red pencil on them. This shoot was needed because the manually marked drawings were being sent off to a contractor who would be using the markups to update the original CAD drawings. Concern existed that the drawings might be damaged or lost in transit or before the changes could be made to the CAD files, and also to be able to do a comparison check to assure that the contractor had made the changes correctly, so a record of these markups was needed for safety. Actually seven of the original prints did end up needing the use of the photo files of them for some reason not disclosed by my contact, but he was very happy with my work.
Since the walls of the office given to me for use were made of metal modular partitions, I found a wall where the ceiling fluorescent light ran parallel to the wall and out about 2' from the wall surface. This provided very even light on this wall surface. I then hung the drawings one at a time on this wall with magnets to hold them flat against the wall. With the camera on a tripod and positioned correctly, It only took a few test shots to get the camera adjusted for good results. Then, using a remote trigger for the camera and a large table off to the side to hold the prints in two separate piles, I was able to just place each drawing on the wall one at a time and trigger the camera with the remote. No flash was used at all. The ceiling light was more than adequate, as long as the magnets were holding the paper perfectly flat on the wall. I was able to complete this shoot in one afternoon with no help from anyone. This took place over 10 years ago, so I don't remember the camera settings or even which digital camera that I was using, but all of the resulting image files were in jpeg and about 1/2 meg each in size. The shutter speed was slow, like about 1/25 second, so no flicker problems resulted from the light. I made duplicate CDs of the image files, kept one, and gave the other to my customer contact, after assuring myself that I had a good file for each of the original blueprints which had page numbers marked on them, so visual identification was easy.
Charley