I have not seen java epub toolchain; however, I had great success with Sigil.
If the goal is to make an epic, I would let Sigil go. Before I used it, I manually rolled my epics (with ant build.xml automation).
If the goal is to create a java-based tool binding, then this should not be terribly difficult, depending on how much validation and pipelining you want to do. Personally, I will start by writing an epub viewer.
As for the parts of the PDF, I just embed XHTML. There was no need to embed PDF yet. As for the epub check, if all the xml are valid and there are no dangling links before starting zipping, you will have a valid epub.
Edwin buck
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