I completed most of the Drupal upgrade last night. The bad that has to be fixed.... permalinks are broken as a result of the change in the architecture. For the moment I've made this change in node.module to get the # to appear again (lines 526-529 which were 526-528). However older permalinks are broken for the moment.
// if ($main == 1 && $node->teaser && $node->teaser != $node->body) # Comment out to Put Permalinks on all nodes
$links = l(t("#"), "node/view/$node->nid", array("title" => t("Permalink to this posting.")));
Next I'll look at either mod-rewrite or a php script to allow the addressing of nodes without the argument based form of '?" since search engines don't follow those links as well. Read more about Good and Bad of the upgrade