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Just got the 2006 LS2 from a GTO started up tonight. All is pretty good except for a P2138 code and no throttle response.
I'm using a C6 corvette pedal. I checked the pins at the plug for the pedal and I'm getting 5v reference voltage at 2 pins. I happened to have two of these pedals laying around and plugged the other one in with the same result. When the key is turned to the "on" position, I can hear the throttle body make a click noise and that's about it. The engine starts perfectly.
I'm using a harness built by BP Automotive which is a fantastic harness builder that provides outstanding service by the way, and I'll be calling him tomorrow of course. Just looking to get a head start on some info if possible.
When the key is turned on, the throttle body butterfly flickers very quickly one time...just a little bit.
For additional info, we checked each pin at the APP:
White/Black: 5 volts
Dark Blue: pulses very fast
Brown: solid ground
Tan: 5 volts
Light blue: pulsing 1.8 volts in increments of 7 (it pulses 7x, then pauses, then 7x, then pauses and keeps going like that)
Purple: solid ground
Im having similar issues with my ls2 swap from a gto using stock ecm/tb/pedal. the car will start and idle but the throttle is almost in a limp mode, very little happens when you mash the pedal. If you pump the gas once right when the engine starts, it seems to work almost how it supposed to?
If I recall what I did, look at the connector at the TB. A - C top row, D - F bottom
Pin A Brown Circuit 582 TAC 2
Pin B Yellow Circuit 581 TAC 1
Pin C Black Circuit 1704 Low ref
Pin D Purple Circuit 485 TP sensor 1
Pin E Grey Circuit 1688 5 v ref
Pin F Dk Grn Circuit 486 TP sensor 2
If I recall what I did, look at the connector at the TB. A - C top row, D - F bottom
Pin A Brown Circuit 582 TAC 2
Pin B Yellow Circuit 581 TAC 1
Pin C Black Circuit 1704 Low ref
Pin D Purple Circuit 485 TP sensor 1
Pin E Grey Circuit 1688 5 v ref
Pin F Dk Grn Circuit 486 TP sensor 2
Try switching A and B.
I swapped the Brown and the White/Black wires on the pedal connector per the guidance of my programmer/harness builder. The car wouldn't start in that configuration.
The plug at my throttle body is labeled as follows. "Top" represents the row of wires that is facing forward, away from the engine.
I found Painless wiring instructions regarding the pedal part number 25835421 and at least for their harness, this is what they had to say about it:
The C6 Corvette accelerator pedal can be used with the harness. The GM part number is 25835421. This pedal is made from steel and only has about a 1.5” offset to right side. Pictured on the next page you can see one of these pedals mounted in a 1978 Camaro. Notice that we had to build a custom mounting bracket in order for the foot pad to line up with the brake pedal. Now, if you choose to use this Corvette pedal you must move two wires in the pedal sensor connector. See page 36 for direction on how to do this.
Page 36:
Repin connector to show:
A - PU
B - L BU
C - TN
D - BN
E - D BU
F - WH/BK
And that ^ is how my harness came originally.
My buddy plugged his HP Tuners into my car and I got this info:
Type: Pontiac GTO (V8) 2005 (funny because I thought this was from a 2006)
VIN: 6G2VX12U45L438010
VCM ID: 86YLPJM0505212P4
VCM OS ID: 12596734
On LS2.com, a guy had a similar issue and wrote this:
"It turns out that the pin out of the accelerator pedal in a late 2006 VZ GEN4 LS2 with an E38 controller is different to both 2005 2006 GTO and later LS3."
He then posted the schematics but I don't have access to those photos.
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First Startup: P2138 and no throttle 
