I'm a bit late to the game, but I'll throw out there that one clue that does lend some support to the road grime theory is that the CAI prefilter is covered in the stuff as well. If that box seal actually seals against the hood, how else would the stuff coat the prefilter than if it was coming from outside the engine compartment?
When was the last time the engine bay was cleaned prior to noticing this grime under the hood? Was any sort of "dressing" used the last time the engine compartment was cleaned/detailed?
-Rod