This is quite a common thing with the N12 engine. I had the same thing and it took me ages to get to the bottom of it. A few things can cause this but all relate to the Vanos system. Did you do the work yourself? Did you use a good timing tool and is the timing spot on? Is the engine management light coming on when it makes the clunking noise? If so, do you have an OBD reader to read the fault codes? Also, how many miles has your car done?
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