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I also have an E60 with M54 3.0 liter, and know the M54 well from several cars.
Shaking could be sticky Vanos. If no CE codes flip or EML light comes on, then replace all the vacuum lines, ICV + rubber sleeve, and if needed, intake boot.
Plug into a data reader and logger to observe what's going on with spark advance and Vanos behavior and verify all injector activations. Good luck!
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And you may ask yourself, "Where is that large automobile?"
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