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Now that the engine and transmission are back together, hook up the engine harness to all the sensors.
One thing you will notice is that the engine harness on the 5s-fe engine went into the rear trunk from the driver's side. The 1MZ-FE engine harness will want to go into the trunk from the passenger side.
But the body harness relavant wires to the ECU will still want to come in from the driver's side.
SO, you need two holes to the trunk. Get a mouthpiece. Get a hole saw, I think about 1.5 "- 2", and drill a hole in the pass side of the trunk wall. The rubber gasket that should still be attached to the engine harness, will make the hole water tight.
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