There's documentation on the classloader in the Tomcat docs, that is fairly complete.
As for your trouble with *some* parts relying on 1.3 and other parts needing 1.4, are you *sure* that they depend on 1.3 ? I'm fairly certain Sun went to great lengths to preserve 'backward compatibility', such that programs written under 1.3 will also function under 1.4. If the dependancies you're talking about are XML parsers, you're in luck. There is a good section on how to use the 1.4 'endorsed jars' mechanism in the Tomcat docs...
Here are the Tomcat Docs on
Class Loaders [ June 13, 2003: Message edited by: Mike Curwen ]