Wow, these are terrific responses, and very helpful! So to address a few questions...
1) I will be able to visit / spend long hours over several months at the location, since it's at my university and there's no problem with access. So I can work out the bugs very early (before I get very far into shooting) and then just go at it until I'm done.
2) Artifacts will vary in size somewhat. Some are small - say, roughly the equivalent of the diameter of a quarter or half-dollar - and others will be fairly large, maybe the diameter of a tea saucer or small pie plate, give or take. Most are somewhere in between. They are all stone, antler, or bone.
3) Lighting should be relatively all right - it's a well lit room, but I also have access to several light sources that can be positioned as I need them. I may look into a small light tent to diffuse the light a little more homogeneously, but I've taken photographs in this setting before and the lighting was quite sufficient for good images, I just didn't have a decent enough camera before (or the go-ahead for the project) to take photos of everything.
4) I have to admit that I'm trying for a relatively adaptable setup, since this is a one-time thing (grant-wise) and I hope to be able to continue to use this equipment for other projects down the line, both of a similar nature and in a more field-type setting. The tripod seems a bit more adaptable for that kind of multi-use arrangement, but I'm certainly considering other options as well.
5) I had been considering RAW format. I'm definitely aware of the problems of JPEGs, and I'm absolutely not interested in those kinds of artifacts, so to speak.
Last... I'm anticipating having the camera set around about 10-12 inches above the photo board / platform / artifacts. I do intend to take measurements from the images - in fact, I hope to take most of my measurements from the images if possible, to limit the amount of handling I have to subject them to.
I just got back from a trip out to a couple camera places, and was able to talk to some folks about these things. One fellow suggested a 50mm macro lens (in the 4/3 format with an adapter) might be the way to go if I went with a micro 4/3 body. I'm not sold (by the way) on a micro 4/3 camera, but the size is appealing - the larger DSLRs are just a bit much, and could be a problem if I needed to take them into certain field settings. But ultimately it's about the data, not the style of the camera.
Thanks for all the comments so far, and for any additional advice y'all can offer. It's very much appreciated!
EDIT: One additional question. I intend to set up a photo backing / board that will permit the easiest removal of background for publication, but I don't want to use something that will show dirt easily or quickly. I had considered using a green or blue (roughly like the colors of the green- or blue-screens in movie fx) matte-finish board. Is there any chance that this could throw the color balance of the photo off? I've noticed less expensive cameras have a tendency to adjust to the light / color in the image, and I want to ensure consistent color balance and lighting, and make it easy to process these images (Adobe Photoshop) and remove unwanted backgrounds for potential publication.
How would you guys suggest dealing with this? Am I on the right track or is there something else I should be considering?