As for finding your information... (ie, what used to be in the little box)
If you look up at the top right, you will see a number in parentheses next to your name.
This shows you *both* the number of Private Messages and the number of updated favorites you have (combined). Hovering your mouse over your name will give you a new dropdown menu, where it has links to places for you to go, as well as the specific number of PMs and updated favorites.
Dolby temporarily forgot to add support to the "AUTHOR" area (next to your name, if you're an author) for bug reports and feature requests, but they will be added shortly, and will display the exact same way as PMs and favorites, only in the "AUTHOR" block/menu.
Cairenn's news post should highlight some of the changes made to the layout of the site. But that should get you guys set for now.
If there's anything else that has been moved and you can't find, or anything else you have questions or feedback on, please feel free to post it in this thread.