So I ripped out the menu system and I thought I will be able to put it back just because I had an idea (and some code) of how the router will work essentially and how the navigation block would work. I was wrong. There was an immense amount of work to be done to complete the menu conversion and it's very likely I would not have been able to do it in any timely manner or maybe not at all. But Peter Wolanin stepped up and did a significant portion of this work, Without him there would not be even a Drupal 6 beta 1 at this point.

We learned something important here: it's never easy. It's great to have skeleton code but you must size up your work before running away with it.