Recently got my 2005 6.0 egr deleted and plugged in my SCT x4 tuner in with a street tune and the egr turned off (didnt know if that mattered) and it wont roll coal at all. Exhaust expands from 3.75 to 5 with a muffler on it and was bulletproofed with the heads rebuilt. Not sure whats going on

 

Maybe try a more aggressive tune

 

Most the tunes now days are designed to provide less smoke.