So here's a rough outline of what I've done to my child theme:

Modified the header.php file to remove the erroneous hfeed microformat that was being put on all pages.

Changed the archive.php page to add h-feed and hfeed to create the appropriate feed pages (I need to doublecheck this in an actual reader, but it looks good on the page and seems to parse properly.)

In the functions.php file, I've wrapped the_content in e-content, wrapped the_excerpt in p-summary

In the functions.php file, I've added a filter that will add h-entry to the correct place.

The nice part is that this means I can use Brid.gy Publish to syndicate to Twitter. It also means that my replies to sites should also properly remove the reply context and only send my reply content. There are still a few small niggling things to clean up, but these always seem to be the most difficult. Hooray!