Context paths are missing, and connecting to Confluence via Apache's mod_jk fails. However, connecting to Confluence using http://localhost:<port> works.
Confluence 4.0's upgrade manager does not copy over any modifications from the previous installation's server.xml, including AJP connectors, context paths, etc.
Ensure there is a backup of server.xml before upgrading to 4.0. After the upgrade, proceed to replace the server.xml in Confluence4InstallationDir/conf with the backup copy.