I have a 03 dodge 3500 with a fass 150/150 a Dr performance predator, and a duel feed line. Most of the time it runs great. Every once in a while it will just not run right. It is drivable but a serious loss of power. It seams to be happening more often. Another thing I don't know if this is related or not, but since this has been happening there has been a few times that it has had a rough idle.

 

It could be the pressure relief valve is either weak or the box is popping it causing it to go into a sort of "limp" mode.

Second thing to look at is the FCA or fuel control actuator. That can have similar symptoms.