There are 4 things contributing the BLACK oil in a 04. 5-07 5. 9. The cam, turbo, pistons, and tuning all create the aforementioned in-cylinder EGR.
On my truck I have replaced the cam and turbo, and run aftermarket tuning that advances the timing and removes the 3rd injection event. The only thing left on my truck is the OEM non-reentrant pistons as far as the in-cylinder EGR is concerned. My oil is always BLACK as soon as I change it, even before starting the truck. I also run a 2um Amsoil Bypass filter.
I did a little experiment at my last oil change. Before I dumped the oil I put a 1/2 bottle of Amsoil Engine Flush in and ran it for 15 minutes. I then dumped the oil, blocked off the bypass, and changed the filter to a cheap one. I added 3 gallons of Delo, which was BLACK as soon as I checked it. I then drove it 4-5 miles to get it hot and added a full bottle of Amsoil Engine Flush. I idled it for 15 minutes and dumped the oil. I let it drain for several hours. I then changed the filter to a normal one and filled it back up with Delo again. I drove it this way for 100-150 miles and then drained it. This time it drained for a long time, with the block heater on. I also jacked up the truck front to back and side to side and got even more oil out. I also removed the valve cover and used a syringe and sucked all the dirty oil out of the brass freeze plugs on the head, and then poured about a gallon of fresh oil over the rockers and thru the head to push more dirty oil out of the block and into the pan. When I poured that oil I had the plug in the pan so the new oil was caught, I then ran the started and pushed the clean oil into the cooler and the dirty oil in the cooler out to drain. I then drained it again for a few hours until it quit dripping, with jacking it again to get more oil out (a surprising amount came out, maybe not a huge volume, but more oil did drain).
While it was draining I changed the filter to my usual Donaldson ELF7349 and hooked the bypass backup and put a new EaBP-110 on. Once the dripping stopped I put the plug back in and filled it with Amsoil AME, my usual oil. I normal put in just under 3. 5 gallons, but this time it took the full 3. 5 gallons, so I defiantly drained more than usual. After letting it run for a few minutes I checked the level, and this is what I saw.
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So the oil in a 04. 5-07 CAN be made clean, but it didn't last long. When I check the oil at 50 miles it already had a minute tinge of black to it, but still very clean. I didn't get to check it again until about 1500 miles and it's back to BLACK. It's a cleaner BLACK than normal, but still nasty.
So, based on my experience it's the piston bowl design that contributes to most of the black oil.