Code suggestion

I was looking through your module for ideas, and I came across

function menu_node_edit_menu_alter(&$items) {
  // We need to account for all parts of this item, in case
  // other modules interfere. See http : //drupal.org/node/469998.
  // We only alter the access parts, however.
  $items['node/%node/edit'] = array(
  ...
  );

Have you considered replacing that section with this?

    $items['node/%node/edit']['access callback'] = 'menu_node_edit_check'; // Our callback.
    $items['node/%node/edit']['access arguments'] = array(1); // Our arguments.

Instead of replacing $items['node/%node/edit'] with your version, just set the entries you need. It seems to me that this would solve the problem of discarding changes that may have been made by other modules.