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The HICAS harness is a bit different due to a couple of extra plugs for the HICAS thing on the lower passenger side frome rail, and the ABS unit.
Other than than, I don't know of any differences, unless the auto and manual harnesses are different.
I'm sure you can use any of the available harnesses, you might end up with extra plugs depending on the harness you get and the chassis you have.
Maybe a wiring guru will chime in to set the record straight.
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