This became too long for a comment, so I'll post it here.

A partial solution to this problem, that at least allows manual alignment and stitching of the tiles after the fact, is to make a rectangular stencil out of flexible plastic or card. On all four sides of the stencil, include distance markings. Place this around the area that you're photographing as you snap each tile. By using a flexible material, the stencil should match the contours of the stump.

A quick and dirty illustration of what I mean:

You say that you are taking a macro shot, so the distance scale at which you're photographing is probably small enough to treat the stump as flat, albeit at an unknown angle, in each individual photo. If this approximation is accurate (i.e. your photos are small enough) then the two distance scales provide enough information to rescale/resize each mosaic tile image to the same relative size. You can do this by rotating and rescaling both axes of the image as necessary. You can then stitch these `mosaic tiles' together in an automated way (the methods of which are beyond me, although you hint that you are already doing this) or, as a last resort, you are able to do it manually.