I'm not that conversant with Jeeps but the symptoms you describe seem to point to overfueling as already said, in the days when I used to run petrol engines, that would seem akin to driving with the choke on, ok when you first start up from cold but running very rich when warm, that would cause it to run badly and make the plugs black.
I don't even know if modern petrol engines have chokes on them, but if they have that's where I'd look.
Sorry about the ramblings of an old bloke ;) and hope you get it sorted soon :D