BG your comment about biodiesel combusting slower than diesel would fit nicely with the hypothesis that the flywheel is the culprit. A heavier flywheel would tend to dampen the vibration caused by quick combustion.
On a similar note, I have noticed a dramatic increase of what I will call 'lurching' since I "upgraded" to 265 nozzles. What I mean by lurching, is when I am driving slowly in 1st or 2nd and accelerate gradually, the car will lurch violently (like they do in movies when a kid is learning to drive a stick shift). This only occurs under light to moderate acceleration. Heavy acceleration does not yield the same results.
This lurching is what initially got me thinking about clutch springs being too light. I suppose that I have somewhat more torque than stock. Significantly more at lower rpms do to the VNT swap.
I just wish it drove more like my Scout. You can lug that thing right down to idle and get NO vibration whatsoever. Not that I seriously lug my engines, I just like to shift to a higher gear when cruising around under low torque conditions... saves fuel.

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For Sale: 1982 MB 300TD
1995 Chevrolet Suburban 6.5TD

Sold: 1980 IH Scout Traveler- Nissan SD33T Diesel