LS Swap Troubleshooting..no pedal response

[shearjs]

We're just about to wrap up our 70 GMC with an LS swap, and have been doing some trouble shooting by just driving some shake down miles. It's been driven around 40-50 miles with no issues, and then this started. When the truck gets up to operating temps, it starts to develop a slight miss, and then the accelerator pedal stops functioning. The computer shows codes for the pedal sensor and for the throttle position sensor. We tried replacing the throttle body, and the pedal sensor, with no improvement. I'm kinda stumped at this point and open to ideas. The engine is a LQ4 6.0L from a 2004 Silverado 2500. It has a reworked stock harness and a basic computer tune eliminating VATS, emissions, etc. Any help would be greatly appreciated. Thanks.