So there are NO check engine lights and no codes. Using a BMW-specific scanner?

No timing codes, no vanos codes…nothing…perfectly clean, just these running issues you stated?!?

I can think of many things it might be, but we all do a disservice tossing out ideas when we are just blind. (Like the vanos solenoids sludged up, due to oil issues and sitting, now causing timing…)

Codes. Or pay “the” mechanic…or find another shop… $1000 seems way unreasonable, so I’d move on.