We need to get some data logs. Without data, we are all just guessing. Sure, we might stumble upon the problem and solution, but we might not...
If the truck is tuned, it might be setting the overboost limp mode and NOT setting the check engine light, depending on how it is tuned. It might be a good idea to verify the tune is stock before continuing, since you believe this to be a stock motor. If the tune turns out to be modified, then the solution is to either return it to stock, or modify it further to work for your setup.
Let us know the data when you hear back from your friend with the scan tool, because I'm out of meaningful guesses at this point.