1) How can I propagate SectionEx URLs to the entire Joomla! framework? I would like them to be generated on the FrontPage, for the Latest News module, and so on.

Riccardo Budini provided a great trick and explanation on how to achieve this. It will take you less than 5 minutes. Just check his article at: http://www.provisum-studio.com/sectionex-urls.pdf

2) My Print and PDF Icons don't wotk with SecionEx if SEO is enabled. How can I fix this?

Unfortunately you will have to add a few lines to the Joomla! core code. Go to "..\components\com_content\router.php". There you will see the "ContentBuildRoute" function. Just add the following few lines at the beginning:

function ContentBuildRoute(&$query) 
{  
     // ugly hack for SectionEx
     // the following lines will make your PDF and Print Icons sing again :)

     $menus = &JSite::getMenu();     
     $myMenuItem  = $menus->getActive();     
     if (strcmp($myMenuItem->component, "com_sectionex") == 0)     
         $myMenuItem->component = "com_content";

     // end of SectionEx hack       
... 
}