I think that some issues with the interface can be solved simply if you have the "HLP" tab open by default. This would solve problems 1 and 2 without re-arranging anything.
#3 - Just "Wiki", "Projects", "Links"?
Personally I'd like to see the menu bar tilted to the left (just like it is right now on the forums), and order highlights and news vertically rather then horizontally. Again, similar to the forum layout. I like the forum layout, and since that is where the most time on this site is spend, ensuring that the main webpage mirrors the look and feel of the forum would go a long way IMO.