*From memory (that's now 3 years old), body mount locations (IIRC 2 additional on x-cab vs. singlecab) and wiring harness length/branch differences are the two that stand out in my mind right now. Honestly though, once/if you lay a single cab or Runner frame side by side it all is pretty straightforward. The big differences you need to be concerned with are 22R vs. 3VZ engine mounts. You can slice off salvagable body mounts and relocate them to the new donor frame.
I'll see if I can find the diagrams if someone doesn't clip them in before I can.
I wonder if the internal reinforcing plates are different at all, like the one's inside of the #2 mounts on the 4Runners that are a z-sort-of-shape.
I've never bothered to look inside the 4x4 frames but I know they are definitely not in the 2wd frames and why if guys get them they're OK to do a SAS on but need a ton of plating added to give strength.
Let's see pics of this disaster before you're all done with it, in fact a ton of pics would be sweet so the next guy searching get's your writeup and if it's good enough we can stuff it over in the FAQ's.