For anyone reading this trying to figure out how to wire their 5-speed swap, I created a new thread a while back explaining all of this. Everything you need to know to properly wire your swap can be found here
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5-Speed Swap Wiring Diagram
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1999 4Runner Limited - 5VZ, 4wd, Factory E-Locker, Multi-Mode, 5-speed swap, Armored, Icons, 295s (
thread)
2001 Tacoma Xtracab - 3RZ, 4wd, 5-speed (Daily Driver)