Eventually my TAR from R12 Upgrade Fun & Games suggested that I rerun autoconfig for my DB Tier and I ran into another problem. Since it was not related to the original TAR, I opened a new one and put the original TAR in "Waiting for Customer" state until my new problem could be solved. Interestingly enough, the root cause of the new problem was that I had my $ORACLE_HOME in a different location than rapidWiz thought it should be, so rapidWiz put my newly created context file in the wrong location. I was trying to run adconfig.sh with an 11.5.9 context file, which kept giving me an error about version compatibility. Fair enough, I was back on track in about two days.
So I went back to my original TAR and posted that while I ran autoconfig on my db tier and bounced all my services, that still didn't fix my issue.
And I wait...
While waiting, I found Stephen Chan's blog that pointed me to Oracle Application Server Diagnostic Tools and Log Files in Applications R12 (ml note 454178.1). Definitely something to test, SINCE I'M JUST WAITING.
...to be continued... (hopefully)