Can you look at the afrs of each bank with uprev and just double check that they are in spec? I am still thinking one of the banks is messing up in one way or another and giving you that vibration.
I know its not the same engine or even close to the same. But on the Chevy diesel engines some of the models are known for their injector harnesses rubbing through causing 2 or more injectors to stop working, and when that happens it 100% looks like the engine just popped. Its amazing what a couple dead cylinders do to the harmonics of the engine.
My train of though is if you see if the bank is running very lean (injectors) if you see it is running very rich (spark). If both banks seem to be pretty close to each other than that train of thought goes out the window.
Just another thing to try.
Goodluck
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