if all these issues are being caused by dirty throttle body, is that covered under warranty? How much when out of warranty? How frequently should it be done?
I still think it is something to do with the Aux bypass, an intermittent short from it as it sounds like thats when it started.
...I'd inspect everything you touched...
I bet it;s from the aux mod you did. I remember reading here about some unique electricity circuit that ne FX has . i think it was a thread about the alarms with remote starters being installed on new FX's . where some guy said that installing it is very undesireable since sooner or later it will short circuit the whole car.