Ok this is what I did for the low pressure side to prime the system.
I disconnected the line at the HFCM and turned on the pump it self primes it's self in 10 seconds. I let about a gallon come out to insure there was no air. Then I did the next line up and flushed it out also. Next I hooked up the bango bolt on the fuel bowl and filled the fuel bowl. I suck out all the fuel in the fuel bowl three times. Then put my new filter in and filled it. I did on have that special fitting to go on the back of the fuel cooler so..... I took the shreader valve out of the other fitting and hooked up a tigon tube to it and flushed 1 gallon out of it also. Plus looked for air. Once no air I disconnected the tube and place my finger over the hole until I could get the shredder valve back in. This is all Low pressure side.
For the high pressure side I just cranked the truck 3 times the first two for 10 seconds, it fired right up after 5 seconds on the 3rd crank. Then I ran it for 15 mins and checked for leaks. I have a Auto Enginuity so I ran rail pressure up to 17000 psi to check for leaks. I found NONE!!!!! (AE only goes to 17000) All items on the High pressure side were replaced.
I was really careful on the Low pressure side to ensure I had no old fuel left in the system. Plus I brake cleaned every line and blew them all out with 80 psi of air. Took out the HFCM replaced the pump and cleaned it all up. Dropped the tank wiped it out cleaned out all lines.
The truck seems to be happy once again, it runs very smooth and quitter now. I think I have just about all the air out of the system. I am going to check short term fuel injectors today, because the other day on the 1st fire up I have #5 at +8 and #6 @-13. I may have gotten 2 bad injectors all others were +or - 3 to Zero. However I did check it again after I drove it and #6 was down to -10. I think I still had some air in the system. So I will check it later on today once I have some more miles on the truck.