So I was thinking about your idle problem. New 90mm throttle body and intake swap. BRAF is unusually low, and it hasn't changed since parts were put on. It's almost half what should be expected.
braf.png
See here in the log. Engine is up to temp. As rpm is decaying to idle MAP increases. IAC closes and no more air can be subtracted. Idle spark begins to compensate.
idle airflow.png
First step is making sure the throttle is closed or barely cracked. Next do a TPS relearn. Turn ignition on then off. Unplug TPS and IAC. Turn ignition on for at least 5 seconds. Turn off then reconnect.
If the problem remains check for vacuum leaks. TBSS intake was just installed, and I hope you used new gaskets. Check the vacuum lines. There could even be a leak in the brake booster or the PCV valve is stuck open.
Monitor IAC counts to indicate if you've fixed the problem.
Also, the knock sensors. Did you end up replacing them with genuine parts and torqued to spec? You're getting KR where there shouldn't be any.