You can run the splunk btool --debug tool. I had several "No spec file for: ... .conf" entries after moving from 5.0.4 to 6.2.3. Then I remembered I had some sandboxing app with copies of ALL the default configuration files in it. I removed the app, restarted Splunk, and everything appeared to work after that.
My guess is that there are some incompatibilities between the different configuration stanzas and syntax of 5/6 and that while the migration will overwrite the conflicts in the /default paths, it won't touch conflicting settings if they are somewhere else (i.e., /apps). I thought Splunk 5 actually included some deprecated setting stanzas from 4 to avoid this but it doesn't seem to be 100% true going from 5 to 6.
