OK, after puttering around some more in the bar, I realized that the "Stack Exchange" logo was a menu, and both missing links were under it. Not the height of convenience but a far better situation than not being available at all.
This concern was brought up on Main Meta:
Please make the stickiness persistent, at least from main to meta if not network-wide
I know that a network-wide flip for the stickiness is an, uh, sticky point, but I was pretty surprised to find the top-bar to stick to the top of the screen on meta.SO after I'd disabled that feature on SO itself. Add additional ...
Stack Exchange Top Nav Choices
I just came across a userscript that allows for customisation of the top bar across all sites, called Stack Exchange Top Nav Choices. It doesn't have all the cool features of Stack Overflow Extras (mentioned by Valorum in a comment on my question), but unlike Stack Overflow Extras it currently works with the new top bar.