2000 Dodge Ram 2500 Diesel - Mysterious Knock on VP44 Dodge Cummins!

LINK TO THE VIDEO


Hey everyone, sorry for the long read but please God read it and help me!!
I've been dealing with a persistent and frustrating issue on my truck for years, and it's seriously driving me crazy. As a mechanic, it really eats at me that I haven’t been able to solve it. I'm absolutely racking my brain here, and I'm hoping someone can offer some insight I haven’t considered.


The Problem:
My truck has a terrible knock at idle that’s so harsh it literally shakes the inside of the cab. It’s loud and clearly audible, especially in person. The knock doesn’t seem to increase with RPM—it’s primarily noticeable at idle—but it does affect the exhaust note, making it sound choppy (you can hear this clearly in the video I’ll link).


What Makes It Go Away (Temporarily):
Here’s the strange part:

• If I unplug the VP44 connector and supply 12V power directly to the pump, bypassing the ECU entirely, the knock disappears completely. This made me suspect it’s related to ECU inputs or sensor feedback.
• Using my scan tool, I can disable ANY injector and then re-enable it. The knock then goes away for about 10 seconds before coming back. During those 10 seconds, the engine runs smooth as butter—no shake, clean exhaust note.

Watch the video and you’ll see what I mean. When I cycle an injector, the knock vanishes for a moment and returns sharply—you’ll especially hear it in the exhaust.

Parts I've Replaced / Things I've Checked:
Here’s what I’ve done so far (this issue predates many of these replacements):

• Replaced VP44 with a known good used unit from a running truck
• Replaced crank sensor and verified wiring from ECU to sensor
• Replaced MAP sensor and verified wiring to ECU
• Installed brand-new injectors (again, issue existed before this)
• New alternator (unrelated, but noting for completeness)
• Installed AirDog Raptor and Beans Diesel sump – fuel pressure is spot on
• Swapped ECUs from a known good truck – no change
• Verified APPS wiring and voltage – originally low (~0.34V), adjusted to 0.5V as per MoparMan's advice
• Checked IAT sensor and verified voltage/wiring to ECU
• Physically checked the timing marks on the timing gears - all good there.

None of these changes have made a dent in the issue.

Final Thoughts:
This truck is driving me insane. I know the signs are pointing to some sort of input/communication issue, but I’ve tested and replaced so much already that I’m at a loss.If anyone out there has run into something similar or has suggestions for what to check next, please let me know. I’m open to trying anything at this point.Thanks in advance! 

Note:
I did find a guy on the 2nd gen Facebook page that had the exact same knocking sound and his issue was resolved by replacing the crank sensor. I've done this already, but he did say he replaced his with a cheap amazon one and the issue wasn't fixed, but he tried a name brand one from the part store and it went away.. I ended up buying a Cummins OEM sensor and the issue was not resolved. Still the same exact thing!  

I can't really hear the knock that you are describing in the video. I can hear the misfire when you disable the fuel injector but, to me, it sounds like a typical diesel engine. 

The knock doesn’t seem to increase with RPM—it’s primarily noticeable at idle—but it does affect the exhaust note

I am wondering if the knock is in mechanical relation to the engine cycle or, a somewhat inconsistent vibration. Possibly, an exhaust pipe banging on the frame or something to that nature. Is the knock stable and consistent? Or, does it have an irregular pattern? 

If you have a scope and a piezo sensor, I would try to find a correlation with the engine cycle. If no correlation is found, I would be looking to a loose accessory bracket, engine mount, or heat shield.