The JIRA upgrade at http://www.atlassian.com/software/jira/docs/latest/upgrading.html has an error in Section 2. Configure your new JIRA to have the same configuration as your old JIRA.
I think the second time it is actually referring to jira-application.properties.

Also there is no mention of what is probably the most important file to change:
server.xml on Standalone JIRA where you set up your DB configuration settings.