The old harness is a real pain the ass to take out so most people just clip the stator and r/r connectors off and run the new harness alongside the old as stated previously. If you look at the pictures posted you will see that the yellow wires that run from the R/R to stator plug are 12 gauge. The factory harness yellow wires are noticeably smaller in diameter. Another way to tell is to follow the positive wire (red) coming off the R/R to the battery. On the upgraded harness this red wire splits off with 1 lead running directly to the battery via a 20amp fuse and the other going straight to the starter relay. The remaining black wire on the harness coming from the R/R is grounded directly to the battery.
Rollin