Where did you purchase the knock sensor and sub wiring harness from? When you used a bypass wire did you clip the wire and tie it to the stub going into the computer and at the sensor? In other words was this separate wire totally independent from sensor to the computer? Did you check the pin fits to make sure the female pins are tight at the computer and at the sensor?
There is no other inputs or wires on this line for this system. If you're getting a code 52 the only way this can happen is if there is an open or short in the signal going to the computer. The info wire is a shielded ground signal wire. Do you have an oscilloscope to actually test the signal at the computer? Did you test the integrity of the signal wire to ground to make sure that there was no short in the ground to signal wire? This should not be an issue if you ran and entire separate wire from the sub harness into the computer. This is normally. What I do when I suspect the issue in the original factory harness, totally cut out the factory harness between the computer and the knock sensor. I normally use shielded coaxial cable from RadioShack. If you are certain that this wire was not interfered with or the signal was interfered with by electro-forces from inside the engine compartment because it was not shielded to ground than that only leaves the option of a bad sensor or sub harness. Normally what I do is put oscilloscope on the wire at the computer then use an air hammer and slightly vibrate the base of the block next to the sensor to see if you can create a signal input to the computer.
You're right that makes absolutely no sense. Not even remotely connected. At least you got the car running. Happy new year.