Comparing the 2 harnesses and the trans position connector1 appears to be the same between the original and donor but connector2 is different. (I'm calling them that because I'm not sure what each actually does.)
Been doing some research (comparing pictures on autozone's website, LOL) and they shouldn't be different up until 03 or 04, but it doesn't have that connector either.. I got the donor off craigslist and it's a red/blue harness. It's got the truck injector harness and all the trimmings of a DBC harness.
It looks like maybe they deleted the heavy gauge wiring that was part of the starter relay circuit and used a thinner plug without changing the female end?
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