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.