Very interesting discussion.
I have just purchased my M9 with about 6 lenses. Having the 5DII with L series lenses, and now ZE's, I fully familiar with AF and MF issues. The problems don't go away. I had spend a lot of time, calibrating and adjusting the MFA until I had good results with 5DII.
With the M9 with 3 ZM and 3 Leica lenses, I was noticing a difference in focusing. I sent my camera to Melbourne, Camera Clinic, an authorized Leica repairer, and found that my M9 was front focusing, and 3 out of the 6 lenses were back focusing. Five days later, costing a $700 for all the work everything is full calibrated. In future any lenses just need to be sent, as the M9 is now set to the master calibration.
I have received the M9 and lenses back and what a change. Lenses that I thought were soft, are now tack sharp. Truly worth the effort.
I am now thinking of sending the 5DII with lenses, to fully calibrate the setup.