I didn't fill the truck, but it has over 3/4 of a tank now. With the pick-up just forward of center on the tank, pointing it downhill would more than cover it all. I've considered running independent return lines from the head and from the injector pump to see if it makes a difference.
As for fuel quality, I have run "black diesel" for the past 80,000 miles or so. It's a mixture of diesel and used motor oil, and I filter it to 3 micron. I run it through a 2 filter set up, with the first filter being 16 micron, and the 2nd one is a 3 micron with a water separator. Factory Cummins filter is 4 micron. I don't think that could be it, since I've ran it in this truck just prior to the teardown and VE install. After adjusting the star wheel in the AFC, and turning the fuel screw in, I was really impressed with how it runs. I can't see it being a problem with the pump. I put new filters on the FASS also. I use Wix filters. I've even checked the voltage to the fuel shutoff solenoid.
I'm running out of ideas, but I'm not one to give up.