I'm running into one other problem: the ad that gets injected above the logo is pushing everything down, but some of the elements don't move. I'm not sure why.
Here's a screenshot, you can see the arrows from the breadcrumbs system hovering over the menu:
** EDIT **
I realize now that XenForo actually places the header further down in the code, and then absolutely positions it, and sizes it explicitly. Very annoying, but I'll have to be very careful about what I put in there, and use media queries judiciously.