Upgraded htmlcleaner (newer is always better)
largely improved the cleanup/markdown conversion mechanisms.
The only thing remaining for #2 is a damn working XSLT.

So far, I've tested
http://www.getsymphony.com/download/xslt-utilities/view/20573/
http://fletcherpenney.net/2006/03/markdown_and_xml
and none of them worked with my Java stack.
I must confess that the very idea of rewriting my own totally makes me sick.
But maybe I'll have to go that dangerous way. As a final work, let me confess the first worked way better than the second (and also let me tell you Eclipse XMl tooling may be slow, but it has XSLT debugger !)