Thank you all for your suggestions and explanation. I could already increase performance a lot by skipping some very simple XPath expressions and using the (w3c) DOM Nodes and Elements instead. Some of these expressions must have been evaluated several thousand or ten- thousand times and voilĂ  instead of more than 20 hours I am down to one hour on JDK 1.5. Using JDK 6 speeds things up some more.
Now I know and understand why SAX would've been a faster way to go...

Cheers,
 thomas

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