Parts replaced caused by collision
-High pressure fuel pump ( new take off ) with new gear
The pump seems to create the necessary pressure, but not the right pressure for 600 RPM. If the FPR was disconnected electrically, perhaps some other electrical problems, short to power, short to ground, etc, I would expect to see the pump at FULL PRESSURE, 25K or more, whatever these L5P pumps are capable of, but NOT 13k at 600 rpm.
The ecm was unharmed in the wreck. I also removed it from the truck and stored it inside while the truck was being repaired.
It is the ECM that tells the high pressure fuel pump what the rail pressure should be after receiving input from other devices and sensors. The pump's actual pressure is very close to the demanded pressure as it should be. It seems at least plausible that the ECM just isn't working correctly in determining demanded pressure. EXCEPT that when you first got the truck back together, it ran pretty well, now it doesn't.
You mentioned that the MAF was pretty low. If the EGR valve is closed, the MAF would read about 40 gm/sec. Your reading is pretty far off that. Low MAF would cause the ECM to demand less fuel to the engine, but you are getting more fuel; more demand, more actual. Perhaps your scanner will tell you what is going on with the EGR - is it partiallly open, or fully closed, or fluttering, etc. That may explain the MAF reading.
It has been said many times that it is the correct diagnosis that is difficult, doing the fix is usually pretty easy in comparison. Seems like this may be another case.