I spent some time decoding the new NPC format and managed to get everything working. I also found and fixed some errors in older data sets (equipment wasn't showing up, historical notes were not being suppressed).
Now it's to the audit part of the process. Everything looks correct so far but the MM3 adds a pretty significant number of npcs. Also the update made major changes to the old data, particularly the keywords / origins changed significantly (check out the fire bat).
Also I was alerted to an error in some PHB2 powers, particularly the stupid Warden Wonder Twin powers where the paragon path name is included in the power name. I fixed this.