While the ECU retards timing in the event of knock, it typically does so well after any damage would be have ocurred. If you run a well-maintained machine, you shouldn't have to worry about knock given the level of modification you have going on. Stock fuel system is not going to give you issues based on I/H/E. Perhaps, you might get a tank of ass gas, but chances are you would know that right off.

Keep in mind that the ECU uses input from CMP, CAS, MAP, and even CLT to determine how much fuel to inject, when to inject that fuel, and finally to light it off. It's a constantly changing environment, based on TPS, engine load, ambient air temperature, vehicle speed and what you had for lunch.

I wouldn't be worried about it. The variations you see in your logs are just the ECU making adjustments on the fly. While it's fast, it's certainly not the type of computer that is going to be beating Kasparov at Chess. Know what I mean?