The server.xml file has changed a lot between Tomcat 3 and Tomcat 4 - rather than just being a monolithic server, Catalina is a very flexible way of organizing various server processing objects, so you'll want to read the docs and look at their model server.xml.
To connect an Apache server to Catalina you need the mod_webapp module instead of mod_jserv/mod_jk. Someday the docs for the Apache options to mod_webapp may even catch up with the actual realease software
Your actual web application layout remains unchanged.
The secret of how to be miserable is to constantly expect things are going to happen the way that they are "supposed" to happen.
You can have faith, which carries the understanding that you may be disappointed. Then there's being a willfully-blind idiot, which virtually guarantees it.