It would be nice if you had a laptop with BMW software or maybe the Foxwell scanner that some of the others here use so they could chime in. Definitely get yourself a copy of the repair information. The BMW software often has the repair/diagnostic info and strategies linked-in that come up with the related codes.
Especially since the car has been so well maintained at the dealership and there is a scanner in the trunk and you likely got a good deal there is a good chance that it will be not easy to find the problem(s) and/or the fix will be expensive. You might try running a can of catalytic converter cleaner to see what happens, might give some clues.

And use only brand name premium gas if you aren't already. I bought an E70 last year as a spare vehicle which I am pretty sure the previous owner was using regular and now have run about 6 tanks of gas through it and it runs better with every tank.

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1988 325is (purchased new) sold
2004 X5 3.0 2005 X3 2.5
2008 X5 3.0 (new to me)