I'm helping a friend right now who has a similar problem on his 02 3.0 with 30k miles.

Car has not been used for a while. Put in a new fuel pump and it's running now, but has the trifecta and cog of death lights on. Shifts through the gears but a bit rough shifting.

Scan showed MAF, ABS module fault, and something about CAN torque, didnt see the actual readout.

We're putting in a new MAF first but I have a hunch it might be ABS system related as a few posts in some e39 forums mention it too.

They suggest pulling the ABS module plug and driving around to check, it works for some. It didnt work for us though.

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04 X5 3.0i auto
03 X5 4.6is