Some may have noticed that the CFMX Administrator no longer stores its configuration info (such as settings, datsources, verity collections) in the registry. If you've got tools that expect to find the info there, you'll run into trouble.
The good news is that most of that info is now simply stored as wddx packets in xml files, stored in the cfusionmx\lib directory (such as neo-query.xml and neo-verity.xml). Don't mind the neo reference. They just didn't change that in the final release.
Now all you need to do is learn how to process the xml, or more particularly the wddx packets. CFMX's new XML features should help. I highly recommend David Gassner's 3-part series of articles in the June, July, and August CFDJ for more help on that.
Just as an aside, some may notice that there's also info about your datasources in \CFusionMX\runtime\servers\default\SERVER-INF\jrun-resources.xml. It's not clear to me what the difference is between the info stored in the two places.