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It is fairly simple to make a 4L60E harness from a 99-07 1/2 ton 5.3L truck work with a 4L80E transmission. These same steps will work for an 99-07 Vortec Truck, LS1 99-02 style harness, or 04 GTO harness for that matter (some wire colors maybe different on GTO)  Remember 99-02 PCM's used BLUE and RED pcm connectors, 2003+ use BLUE and GREEN PCM connectors.  The wire locations are the same for all years, so this process is the same no matter what year your truck harness is.

There will be a few changes to the pins at the transmission plug, and at the PCM plugs. 

The first step will be to remove the cover over bottom of the pins on the 4L60E transmission plug.  There is a small plastic tab holding each pin in place, this tab must be lifted, then push the pin over, and out the back of the connector.  (Same process at the PCM.)

You will need to REMOVE 2 wires, and MOVE 1.  Each wire has a label in the rubber insulation. The middle row shown, L,M,N,P,R,S.  Q and O are not used. T, U is the bottom row.

In the picture below, we REMOVE

the WHITE wire, in location S,

the TAN/BLACK wire, in location T

The next step, will be to MOVE the BROWN wire, in location U, to location S where there was previously a wire.  You should use some silicone to fill in the now empty T and U cavity's.

 

That is all that needs done to the round gray transmission plug. It is now ready to plug into the 4L80E transmission. 

The 4L80E transmission has two speed sensors, 4L60E only used one.  You will now have two extra wires, these will be used for the 4L80E's INPUT speed sensor. Attach a speed sensor pigtail to the WHITE and TAN/BLACK wires removed a few steps above. It does not matter where these two wires go in the two pin speed sensor plug.  Polarity does not matter.  The existing speed sensor wires from the 4L60E (purple/white and green/black wires twisted together) will hook to the speed sensor directly above the round gray trans connector on 2wd's, or in transfer case adaptor, or transfer case output housing on 4x4 applications.  The new speed sensor plug will hook to the INPUT speed sensor, located above the shifter shaft on the side of the 4L80E.

That will complete the wiring changes at the transmission end. Now, you will need to go to the PCM connectors, and re-purpose the WHITE and TAN/BLACK wires for the input speed sensor. 

The WHITE wire will be found at the C1 (BLUE) Connector PIN #79. Remove this pin, and MOVE it to C2 (RED or GREEN) Connector PIN #22.

The TAN/BLACK wire will be found at the C2 (RED or GREEN) Connector PIN #42. Remove this pin, and MOVE it to the C2 (RED or GREEN) Connector PIN #23.

The PCM programming must match for a 4L80E as well, I offer segment swaps for 4L80E included in the standard $75 I charge for Gen 3 PCM programming. www.lt1swap.com/programming.htm