Hello Fletch3-
There are many dependencies in a typical voice deployment and they can cause a host of problems in an ungrade, I would make sure I had a good backup, turn off CSA and then follow the upgrade Docs.
For those you want to use the Cisco document "Upgrading Cisco CallManager Release 4.1(3)" it goes through step by step what you need to do to have a successful upgrade. The document can be found here:
http://www.ciscosystems.com/en/US/docs/voice_ip_comm/cucm/upgrade/4_1_3/upg413.html additional information can be found with the Cisco CallManager Documentation Guide for Release 4.1(3) found
http://www.cisco.com/en/US/docs/voice_ip_comm/cucm/docguide/4_1/dg413.html.
hope this helps,
-t