After more investigation, I can't load it from the theme file. I guess that you can, but you have to make some changes to the requires stuff that it is kind of silly. ../../../../ It gets to be a lot after a few of those.
The menu is created from the admin->lib->menu.d-> directory. This can not be included in your theme.
I was unable to figure out how to write that query. If someone could help with that, I would be very glad. I am learning PHP so it is taking me a lot longer than it probably should to figure this out.