Hey @wsnyder2 you do not need to upgrade the Palo Alto App first for it to work with 6.3.1 (provided it was configured properly in your Splunk 6.2 environment) .
That said, with the release of the v.5.0.0 of the Palo Alto Networks for Splunk app there is now an upgrade guide: http://pansplunk.readthedocs.org/en/latest/upgrade.html
Highlights are that there is now a TA (Technology Add-On) bundled with the app - this makes deployment more flexible. That said read the upgrade guide thoroughly as there changes like which index the TA writes to by default (no more "pan_logs" index).
Are you also an Enterprise Security user?