So for the app-<yourWindchillWebAppNameHere>.properties (e.g. app-Windchill.properties) file in Apache/conf/extras, you'll want to modify/ensure two lines:
enableCustomErrorDoc=false
proxyEntireWebApp=true
Then invoke "ant -f webAppConfig.xml regenAllWebApps" from the top level Apache directory.
This will reconfigure all web apps to proxy all requests over AJP to Tomcat rather than assuming some files can be server from the local file system.