Quite an interesting article. It says that knock detection frequency for an LS1 is around 6kHz, which is surprising, but can change with cylinder bore. Dan, I can't recall if you only stroked your engine or had it overbored too? Unless I missed it, it doesn't specifically mention valve train noise but does mention false knock detection (which they probably mean is valvetrain noise).
Can you adjust the gating of when the ECU is monitoring the KS for knock? If so, I was just wondering, unless the knock is occurring at exactly the same time as a particular instance of valve train noise, if the knock sensor was only gated for when knock was likely to occur, the ECU wouldn't be listening for knock outside of the gated period? Although, I know there is the valve gear noise of the other cylinders to consider.
The article also says about single and two wire KS's and the set up method for each. I think you said that yours are single wire (resonant) ones?
Seems it's quite a science