Dark coolant and fuel CM871

[Billcummins6]

Morning,
I have a cm871 in a 2010 Pete 389. The motor was rebuilt and deleted by a shop in North Dakota. Since I have put the VGT back on, put in a reliable tune and got coolant flowing to the back of the head again. My problem now is that when doing my service I found my fuel in my filter was black and now my coolant reservoir is stained black. No blow-by or coolant pushing out the overflow. Any ideas? Is this a head again? I did run the truck for 10 months on the shitty tune and no coolant crossover pipe.
Thanks for your time ,
Bill

[Rawze]

Maybe take a sample and sent it to a lab?.

Black stuff in the top of the coolant tank is usually a sign of oil getting in the coolant. Oil in the coolant is almost always from the oil cooler, not the head.

[Chamberpains]

Also smell the oily substance. Sometimes it will be transmission fluid if the truck is equipped with a heat exchanger for the trans. Though the oil usually presents as a grey brown color, black is not out of the question. It will smell strong like gear oil.