clunky vibrating roar while accelerating

[318i318is328i645i745ix5]

Hi All,
would appreciate some thoughts on a noise from underneathe the bonnet of my X5 3.0d which has been bugging me for some time. The noise appeared when it came back from our local mechanic....need i say more. He fixed the main problem but got left with this noise....

Basically when I accelerate from standstill or low speeds I feel a clunky vibrating roar coming from the engine. It usually appears in the lower gears at around 2000-3000 rpm.

Symptoms:
If the car is in neutral it roars normally.
If I accelerate quickly while in high speeds or high gear then it will give a very bassy quieter vibration.
If I accelerate quickly from medium speed it will downshift and then i will get this auwful clunky roar again.

Interestingly i gave the car a good run where i was consistently doing around 120kph and flooring it at high speeds to reach 160kph. It seems to have settled its throat a little as I noticed that the clunkiness of the roar has been dampened, but it is still there.

By the way my car also whistles when i accelerate slowly, which i thought was the turbo but from reading the posts it seems not.

Could it be the cover which protects engine...?
Could it be the transmission?
It cant be the engine as it is fine when in neutral...

Any ideas ?
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