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Yes, it matters where each blue and green wires go. To determine the proper wires, you can do a continuity test on the green and blue wires. It will require testing equipment like a multimeter/ohmmeter.
To test for continuity, set to either the "ohms" or the setting it will beep when you hold the two leads together.
If your meter beeps, it means you have continuity.
If it is on ohms scale, you will have continuity when it reads close to 0 ohms.
If it doesn't beep , shows OL (open line) or a 1 (infinity ohms); it means you don't have continuity.
The other wire ends goes all the way to the throttle actuator control module (located under the passenger side dash). You would disconnect the harness connector there and check continuity between the various blue and green wires at the throttle body. The green wire from the under dash connector at terminal no. 8 and blue wire at terminal no. 1 should have continuity to the green wire at the throttle body at terminal no. 5 and the blue wire to terminal no. 6. Those are for the motor.