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Welcome, I'm Chris (aka Moose), my normal schedule online is around lunch and after dinner past midnight.
You will need to install a PCM for the 5.9 engine. Your 3.9 1999 PCM thinks there are only 6 cylinders plus the crank and cam sensor readings it receives are not going to be the same from the 5.9 to the 3.9.
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What year model PCM was installed?
Does it run like there is a misfire?
What is the fuel pressure?
Can you remove plug wires one by one to find the cylinder when disabled does not result in it running worse?
Fuel pressure remains 40 even when it stalls?
Will your scan tool show fuel trims?
Have you monitored the CMP and CKP sensors while running to see if they compare as well as to see if either drops out it signal. Have you done a distributor sync with your scan tool?
We have confirmed its not fuel pressure and its not one cylinder to blame more likely all and random.