I'd definitely recommend one of the "mainstream" XML tools (for DOM/SAX/XSLT) over another Perl module, even if this involves a Horrible Hack to switch from the Perl environment to the Java world (a "used coffee filter", or whatever they call it) that the DOM was originally coded for. Personally I'm writing XML/XSLT code for M$oft; IE5 and ASP, so I choose to use the MXSML DOM via Win32::OLE even when I'm coding Perl.

DOMs aren't standardised; there's a lot of space around the W3C spec that is implementation dependent (especially with namespaces). Using something commonplace is good, and Xerces would be a good choice.