Depending on your output image resolution requirement, you have two options as I see it. The first option being the simplest and quickest but not necessarily the cheapest:

1. Use a dSLR with a wide lens (probably a 24mm on full frame or something approaching a 16mm in DX format) and use the specific lens correction option for that particular lens to correct any distortion in post. Mount the camera on a boom arm with a suitably rigid tripod head on it so as to keep the film plane parallel to the subject. Swing the arm up to ceiling height and use a remote trigger to take the shot. Tethering or WiFi will make file transfer a lot simpler and will allow you to leave the camera in place while you swap out each subject. If you have a high resolution camera and decent lens, you will get large, reasonable quality images this way.

2. If extreme resolution and accuracy is required (such as for larger than life reproductions or archival detail levels) you will need to build a sliding horizontal camera rail system that will allow you to take a matrix of images from exactly the same plane and then stitch them together in a panorama. You can do this in such a way that each panorama consists of just 3 linear images in portrait orientation (giving you files with approximately 2.8x the camera's resolution), or you can shoot from a lower height (or longer lens) and take a dozen or more images in a matrix/grid pattern (giving you files with tens of times the camera's resolution). Using this method you will want a lens with minimal distortion to simplify the stitching; a cheap 50mm lens typically is perfect unless you need to focus in the macro range. The rail system doesn't have to be complicated or expensive, but it does have to be rigid and square. Probably aluminium angles and a home made camera brace would work. You could probably build something suitable with little more than a drill, rivet gun, hack saw, file, duct tape and suitable length of aluminium angles; perhaps $NZ150.00 all up (about $US80.00). You could also get away with a cheaper camera with this option (though not recommended), since each individual image represents a smaller portion of the finished image.

If I was doing this as a big project and I wanted the level of detail that you indicate, I would go for option 2 and probably shoot it with a 60mm Micro Nikkor on full frame. I would shoot the entire thing under the best lighting I could manage (minimum of two studio strobes and probably big soft boxes or brollies), and I would shoot entirely with manual settings, using an aperture of f/8-16 depending on subject distance. This would likely require about 6-9 shots per subject and would give very sharp high resolution images with little to no distortion correction required and quite simple post processing. I would script all of the post processing using actions in Photoshop to ensure a ruthless level of consistency.

Edit: I realise option 2 does require manual positioning of the camera from frame to frame, but this can be done very quickly in a routine pattern for consistent results. If full automation is required however, you can get similar rail kits that are designed to drive computer aided cutting tools, so programming it to position a camera instead of a router wouldn't be too hard. You'd probably still have to fire the camera manually unless you wish to rewire a remote cable release and get the program to fire the shutter when in position (by shorting the two required terminals).