No one can really say how easy or much it will cost. It is possible though. I would first do research and find out how much the E46 SMG to 6speed swaps cost in labor and then do research on how much transmissions for n54's cost and what other parts you will need. You will also need the rear diff, pedals, shifter, knob, boot, wiring, coding etc.
If you get this done, please post your findings. You will be one of the first, if not the first to do it, and your project could contribute a lot of helpful information to others.
good luck
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