GM developed a procedure for replacing the knock sensors a while ago.

It involves replacing both knock sensors and both wiring harnesses going to the
sensors.

You then build a small mountain of RVT under the intake manifold to divert the
water away from the sensors wire boots, you might even need to remove the
foam from the one end of the intake manifold.

You then replace both intake manifold gaskets and torque the intake manifold to
INCH POUNDS and not foot pounds.

If you mark all the wiring before you remove it and put it back together in the
same order as what you took it apart, you should not have any problems.

If the check engine light was not on before you started to do the power tune,
then chances are, unless the ports where the knock sensors were, was full of
water, and unless the terminals were corroded, the problem was not with the
knock sensors to begin with - but with the person / equipment that was doing
the power tune.
And now you need to take it all back apart and replace the wiring harness to both sensors.

The water did not get in there all in one day. The problem is a poor design where the water
can get under the intake manifold and has no way to get out.
The top of the engine does not get hot enough to burn off the water sitting on top of the
engine and the foam at the end of the intake manifold does not let the water out.

The purpose of the foam is to give the plastic intake manifold some support on that end.
They are prone to cracking, especially if tightened too tight.

I have diagnosed this problem hundreds of times and the solution is always the same.

As you have already done, take the engine all apart. Clean out all the water before removing
the knock sensors. Clean everything a second time. Put anti seize on the threads of the
sensor. Put RVT on the new wiring harness. Build a mountain on top of the valley cover
which should divert the water away from the center of the intake manifold area where the
sensors are located. Put everything back together - making sure that everything is plugged in
and working.

Job takes two people about 3 to 4 hours to do and a 12 pack of beer. A roll of paper towels,
a shop vac, a air compressor with blow job nozzle, a roll of masking tape, a sharpie marker, a
tool to remove the fuel lines, a 10 mm socket and a inch pounds torque wrench. A long
extension to get the socket on the knock sensor, a 3/8 drive wratchet and appropriate
socket for the sensor - some are 15 mm some are 18mm.
A can to catch the coolant from the MAF sensor. Does this sound familiar?