This is an awesome post with great photos - I have a feeling my E46 has the same issue. I just started showing adaptation codes again - I'd previously replaced the intake boot that solved it.
To answer the above question about codes our tool will see vs. the OBDII - from my personal experience, 1188 and 1189 correlate to BMW's O2 sensor adaptation (using our tool), as that is what is reporting the fuel mix condition.
Using the Bentley conversion chart is a bit misleading, as it takes the generic code, offers a 'translation' to the nearest BMW code, but uses the generic OBDII textual definition. The text definition shown is not the BMW definition, which can send you down the wrong path.
That said, in the case of the adaptation/mixture codes, it clearly lead you to find the vacuum leak that is so frequently the cause of these faults.
Thanks for the write up!