He is saying the plugs should be there. So you can tag them from those plugs and pin them to the proper spots on the ECU connector.
Worth a look since you left the auto body harness in and changed the engine harness.
If not, you can get the CEL of the dash connector pin 4. The stater relay of the relay itself worst case.
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7 3rd gens listed in the build thread (2 are parts mobiles)
Build Thread:
https://www.toyota-4runner.org/3rd-g...os-builds.html
Brillo's Bucket Fluid Ex changer:
https://www.toyota-4runner.org/3rd-g...ml#post3358086
Sparks Plugs Wire and Coil Information:
https://www.toyota-4runner.org/3rd-g...on-5vz-fe.html