You have whole load of trouble coming your way.
"All went well and replacement engine was the same apart from one thing.." and what have you based that decision on ???????
going on the limited info you have provided (no engine codes ) it sound's to me like you have fitted completely the wrong engine.
You say your car is a 2003 which would make it a E46 model. The six cylinder engine for this model range is the M54 and M54TU. This engine has double vanos units and MS43 management system.
If you say the donor engine has the crank sensor on the front crank pulley this would make it a M52 engine ( single vanos also MS40 management system). also it is from a E36 model.
I'm amazed it runs., you must have plenty of unused connectors on the engine loom.
think you need to go and visit spec savers
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