Assuming the harness still has the mounting clips, etc. on it, things should only (easily) plug in one way. If you have a choice (say, on the transfer case switches) match the colors.
You can kinda see the harness routing in these pictures from my 4WD swap:
-Charlie
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'99 4Runner SR5 Auto -
4WD swapped
'89 Camry Alltrac LE 3S-GTE 5spd
'17 Chevy Volt Premier
'16 Honda Odyssey Elite
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