That isn't 'cylinder deactivation', that's just how fuel injected vehicles are designed. 'Cylinder deactivation' is an actual gas saving feature of some V6 and V8 cars where it disables a certain number of cylinders (not all) while at steady state cruising, hence why I'm making it such a point to be careful with using that terminology as it can confuse people.
And no, there is no rumble when they reactivate on our M54's, not on a properly running car at least. The OP said this is happening when coming to a stop going from 1st to neutral. By then the injectors have long reactivated (they kick in once the revs hit 1200RPM or below). I think you're feeling something else, not the injectors kicking in/shutting off. Are your engine, tranny, and diff mounts good condition? Guibo?
In a normally operating engine, you'll never feel your injectors activating/deactivating.
OP, you really should take a video of this happening so we can see what is going on when you say it vibrates.
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I was teasing you on cylinder deactivation, I know what it is :P
But I do feel it; if I'm in gear decelerating, I ever so slightly nudge the gas pedal, i'll feel the engine do its thing. Same when coming to a complete stop in gear, at some low RPM the cylinders kick in again.
It did it before and after I replaced my injectors with cleaned injectors.
1991 E30 Alpinweiß 325iX [SOLD]
2005 E46 Sparkling Graphite Metallic 330Ci ZHP 6spd