Everything seems to be ok, though you have updated Xalan and Xerces? Cocoon 2.0.4 comes with Xalan 2.3.1 and Xerces 2.0. This /can/ be reason, but is not needed to be. I thought more the other way around (using the Xalan delivered with Sun JDK 1.4).
In conclusion I don't have any solution for you, but maybe a workaround: Can you use current 2.0 or 2.1 CVS version? At least 2.0.5-dev shall be as stable as 2.0.4. The important difference for you between the two versions is the switch to the interpreted sitemap engine as default one. So you don't depend on the transformation of the sitemap to Java code.
IIRC: XSP use the same extension method. If sitemap fails to compile properly, same should happen to XSPs.
Vadim
Joerg
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