99 Z28 Help

New motor installed, 99 Z28, ran real rough on initial start. Tuner hooked up HP tuner interface and laptop, did a few things in the laptop and started the car. It ran real good. He unplugged the interface and it started running rough again, he quickly reinstalled the interface and it started running good again. he said to splice a new wire on the blue side of the ecm to the dark green #58 wire to the purple wire on the DCT. but I checked that same wire for continuity and it was good, it rang out, I don't want to cut any of those wires.
How could the engine run good with the interface hooked up and run bad with it disconnected?
Please, need help.