This isn’t exactly what you all are looking for, and it’s kinda hackish, but here’s how I converted a group of my categories to a custom taxonomy.
1) Go into the database and rename everything in the term_taxonomy table that’s currently post_tag to a unique (but temporary) name, like post_tag_temp.
UPDATE wp_term_taxonomy SET taxonomy = 'post_tag_temp' WHERE taxonomy = 'post_tag'
2) Then, using the category to tag plugin, convert the categories you want to tags. Since you’ve temporarily renamed all the tags, what are now tags can be renamed to whatever you want.
3) In the database, convert all tags to whatever custom taxonomy you’ve registered.
UPDATE wp_term_taxonomy SET taxonomy = 'custom_taxonomy' WHERE taxonomy = 'post_tag_temp'
4) Finally, convert the original tags back to normal.
UPDATE wp_term_taxonomy SET taxonomy = 'post_tag' WHERE taxonomy = 'post_tag_temp'
Hope that helps. Oh, and don’t forget to backup your database before doing it.