URL to your eFiction: http://www.wolverineandrogue.com/wrfa
Version of eFiction: 3.3.1
Have you bridged eFiction, if so with what?: no
Version of PHP: 5.3.13
Version of MySQL: 5.0.95
Have you searched for your problem: yes
If so, what terms did you try: internal server error upgrade
Do you have a test account for us?
one can be set up.

State the nature of your problem:
All pages generate an internal server error:
Internal Server Error
The server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, webmaster@wolverineandrogue.com and inform them of the time the error occurred, and anything you might have done that may have caused the error.
More information about this error may be available in the server error log.
Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request.

I backed up the files of wrfa v.3.3.1, and then uploaded the new 3.5.3 files over the 3.3.1 wrfa directory. As soon as I do that, I get internal server errors on all pages, and nothing shows up in the error_logs. As soon as I rsync the old files back over the 3.5.3 files in wrfa, the site works just fine.

I checked permissions, /wrfa 755 and /wrfa/docs/config.php 644, not sure what else to check. Without any generated errors it's difficult to know exactly what's triggering the problem.