[GTLEGEND]

Have you checked the timing? If it slightly retarded, the extra fuel from letting it sit with the ignition on may ignite because there is more fuel in the combustion chamber.

But from your description it sounds fuel related. The fuel filter lines are on correct way (possible on wrong before you touched it and you put on same way?). Have you physically checked the fuel pressure with an external gauge to see what is happening under those conditions on when it plays up?