Build an semi-automated upgrade tool which retains all settings, such as database connection and directories. The administrator should be able to download an upgrade tool, point it at an installation and only be prompted about which plugins they wish to install along with their versions.
This should make use of one-click plugin installer that looks up the plugin website for versions listed as compatible with the current JIRA version, similar to the Confluence Repository Client, then returns the download URLs and versions for all compatible releases of each plugin. It does not need to care about source-code modifications.
There should be a one-click upgrade button in the System Administration tool.
The tools should check for correct database access rights and request them if denied