Put the sub menus on the left, expanded accordion style. This will free up an entire column.
When the screen is wide enough, put the highlighted posts at the same level as the forum title. When the screen is narrower, let the entire box just be on a second line.
Move the "extra" content to the right hand side. Regular visitors don't need to pay attention to them.
Limit their number; they currently scroll down long past the list of posts.
My suggestions on the popular posts.
Skip the division between "All Time" and "This Month" and simply show "Popular".
Then you can tweak the algorithm to pick a nice mix of old-popular, recently active, and new-trending. The list would always be changing, keeping it relevant to both old and new users. (NOTE: always changing doesn't mean dynamically calculated. Calculating the lists once or twice a day, but serving them statically would lessen the load on the forums, and preserve some cachability on the server side.
Introduce a weighting system that would also allow you to temporarily goose the appearance of selected threads when there is a related promotion being offered. i.e. If someone is offering a "How to make bricks at home" book, you give 5-6 "brick-related" posts a +15% weight, and all the "dry stack stone" posts a "-15% weight while the promotion is going.
The problem with "All Time" popular posts, is they essentially turn into a static list that will be ignored by longtime users.
A regular problem with really long lived threads is that the links are often broken, or the users have left.
Nerds be nerding...
The Greenhouse of the Future ebook by Francis Gendron