The flawless system I have running in VMWare is flaky on lettuce. After spending most of the day with this I've reverted to a stock deployment of Cocoon. Using the original settings I've managed to upload all of the EMLS files without difficulty. Monday I'll begin slowly start adjusting conf files and adding/changing functionality to see where it breaks - in this order:

1. add xep to sitemap and jars (xt.jar, XEPSerializer.jar, xep.jar and saxon.jar ) to WEB-INF/libs- this works in the flaky setup
2. restart Cocoon
3. adjust indexer in conf.xml
4. restart Cocoon
5. adjust serializer in conf.xml
6. adjust stock saxon settings (rename to saxon6)
7. restart Cocoon
8. add saxon8 to sitemap and jars (saxon8.jar, saxon8-xqj.jar, saxon8-xpath.jar, saxon8-xom.jar, saxon8-sql.jar, saxon8-jdom.jar, saxon8-dom4j.jar and saxon8-dom.jar) to WEB-INF/libs