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I know nothing about the whipple and the old piggy back. But here is the schematic for the knock sensors. I highly doubt th epiggy system tapped into them...nevermind, I don't know. I know a guy that had a hummer with the whipple and piggy back pcm...he eventually got a divorce and let her have the hummer. It ran like ****. Codes constantly. She was hatin life. Truck would barely run.
The body of the knock sensor grounds to the block - there are no ground wires specifically for the sensors. That's why he was saying that a non-conductive sealer might be causing the problems - if there is not good metal-to-metal contact between the sensor and the block, it could cause issues. There are several ground straps that connect the engine to the chassis, but I doubt that those could be the problem.
Take an ohmmeter and touch one contact to the engine block (valley cover, if you can) and one to the pin on the knock sensor connector behind the intake manifold. Each knock sensor should read somewhere around 100K ohms. If it is too high or too low you know there is a problem.
I got water down in my knock sensor holes and it corroded one of them. I did the ohmmeter test, front sensor came back at 65K ohms and the rear was at 98K or something. Replaced the front one and all was fixed.