The final structures and multiple points of entry and navigation can be worked out later. Here are some thoughts for that time:
Change the current structure (left column) to (right column):
|List of navigation templates||Quick Action Links|
or becoming a minimalist one liner:
Find | Learning Design | Co-Create | Adapt | Share
or better still (user/reader oriented):
Policy Maker | Educator | Learner | Administrator
Oh, I see there are separate handbooks for some of these.
One approach would be to have a series of "trails" through the pages with a compact colour coded button/dots set at the foot and/or top of each page (e.g. learners follow the blue trail, educators follow the yellow, policy makers the green, etc.). In this way you will not end up with potentially several navigation templates on a page.
The idea of color trails is intriguing, and one I'll have to think on. As a note though, the other two handbooks would have their table of contents on different pages, so there wouldn't be multiple navigation templates in that respect.
The "List of navigation templates" was not really intended for end-user use. The idea was to have links to the navigation template for editors, to reduce the number of clicks necessary to edit a navigation template.
Though I could see why it might be confusing for current users.
Whether we change to the Quick Action Links proposed will depend on if we decide on the revised organization for the handbook itself.