Hmm, nice idea.
The only idea I come up with RadicalEdward, is probably the answer that you didn't want to hear...
I just had a bit of a poke around and what I did, was to model and texture it as you've done. Then just go around using the CutFacesTool. Just select all the faces that each boundary will cross, spin the model to face you in the perspective viewport then use the cutfaces tool to make the straight-line cut that defines the boundary of each stone.
Then just go back and remove the extra edges and verts, from there, just pick all the faces of each rock and do an extrusion in or out to suit.
Here's my poxy effort. The faces with the red dot are extruded out, the blue dot faces went in.