People like to ding me for trying to sound like a pro tuner, so take what I say as being from a NON PROFESSIONAL LOL. I'm just some guy on the internet that plays with this stuff trying to learn more about the platform after all
With that out of the way, I enjoy these types of technical discussions.
When I had the new RE engine put in, I started with a base tune and set all the knock sensor values to stock settings including the Knock Window. Testing for STKR I would see 4-6 deg if STKR at 4,000 RPM on a commanded timing of 6 deg. This was running 109 octane, so I knew it was likely impossible to be real knock. The STKR was because the knock sensors would hit right around 2V at 4,000RPM. I started with the knock window and it helped but at 4,000 I still needed to tweak the thresholds a bit. Once I had 4,000RPM pretty well sorted (I may see .5 deg stkr occasionally which tells me the sensors are still listening) I looked for other areas and right around 2,000 did the same thing, just not as severe. Fueling was confirmed and triple confirmed as good at .82 - .83 lambda which is what I wanted for gasoline so I knew it wasn't some lean condition causing it. I even went as fat as .78 lambda just to see if it mattered, and it did not. I have dozens of logs as I dialed in the thresholds over about 3 weeks of testing.
When my original engine failed, I suddenly got 14 deg of STKR and the car fell on it's face. Luckily this happened at the drag strip in a controlled (mostly) environment. After that 14 deg STKR happened, it did it every time after that in the same spot of the run (right after shift to 5th) until the engine popped which happened 3 runs later. On the run it broke, it happened at the shift to 2nd instead of 5th so something was getting worse each time.
Originally we thought the exhaust was hitting or something as the engine sounded just fine, but in the end I suspect a rod bent, a piston skirt cracked, or both. Logs never showed any knock before this happened, but I did find some plugs with the electrodes melted and I think one had plugs with cracked porcelain which some folks believe was indicating knock. I'm not sure if that could have happened during the failure though since the tune was actually very conservative. When the engine failed all the temps shot through the roof and when an engine pulls a bunch of timing things heat up very quickly.
The only other time I had something like that happen, I was making a final pull testing E85 and right at the 4-5 shift got 14 deg of STKR. I seriously thought I'd hurt the motor. Got home and started checking things and found the bell housing inspection plate bolt had backed out 1/2" and the plate was clanging on the bell housing. Put some blue loctite on the bolt, tightened down, and went and made 3 more tests, no more STKR (thank God).