The dreaded "dead pedal" can have 2 sources, APPS or VP44. Pulling the codes from the computer will generally point to the culprit, if it will throw codes. Sometimes you get no codes until the problem is bad enough for the ECM to flag. Intermittent failures that will reset to ECM paramters in a specified time don't generate codes, only limp mode for a short period.
The VP44 has 2 areas that can cause dead pedal, p0216, limp mode and great annoyance. The solenoid responsible for setting the injection timing can fail to work properly and tell the ECM it can't set the requested parameter. The same solenoid can work fine electrically and the mechanical linkage it runs to set timing will fail and cause the problems. The mechanical failure is more common as fuel quantity and quality has a large impact on how the timing system works. That was one of the areas that was updated in the later pumps and rebuilds to help solve the failure problem.