Personally, I would not have put those global navigation links anywhere near the user-specific links. Put global navs next to the GitHub logo, which is the global signifier supreme. All the variations Ryan proposes are merely slight improvements on a fundamentally flawed design. It's like trying to sharpen a spoon when what you need a knife.
The user-specific navigation choices are: all | public | private | sources | forks . You can put these in the upper right block instead.
By the way, you can learn the underlying principles behind this stuff very quickly by flipping through an HCI textbook. Just find a cheap, used copy of a well reviewed textbook online. Ryan's post has nice mockups of a real world example, but barely scratches the surface of the theory. More to the point, he entertains a totally flawed approach all throughout.