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It could be fuel injectors, I knew someone who has a persistent misfire and replacing all injectors with rebuilt ones did the trick.
I would also try swapping the cyl 6 and 1 coils beforehand. If you still have Bosch coils it might just be a good idea to replace all with Delphi/Eldor. You might need to modify the connector or replace the connector with the updated part number if your car is made before 04/06. BMW has a service bulletin about this: SI B12 18 14
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