Looks like maybe verifier output. Without a stack trace, it's hard to know. Also, I would recommend you first get to the 3.2.0 release. It's available in the DL area on sourceforge.
FWIW, deploytool is a cumbersome solution. If you can, you are FAR better off wiring the assembly/deployment into Ant. The ear/jar/war structures are simple to build and are fully mechanized (ie repeatable) with the appropriate Ant tasks. If you are using Ant for your buildsystem, you can integrate the EAR building right into it - even hot deploy it to deploy directory - with no messy dialogs to navigate.
As far as the XML files, look into XDoclet. It generates them (ejb-jar.xml, jboss.xml, web.xml, struts-config.xml, etc) on the fly, from tags in your classes (EJB incl CMP, Struts classes).