Undeploy all extensions using the wex shell (except the kernel)
Remove this line from declarations.xconf
<ConfigurationRef xlink:href="wex/packages/com.wincomplm/wex-kernel/wex.xconf"/>
From a Windchill shell run
xconfmanager -p
Remove the following file
codebase\config\mvc\wex-kernel-configs.xml
Remove the wex-kernel.jar from codebase/WEB-INF/lib area
Remove the entire wex directory from Windchill home directory