I forwarded your suggestions on to the author of the theme and this was his reply:
"Dear Mike,
I have tried everything that was presented in the
thread on http://wordpress.org/support/topic/title-menu-overlapping-popup-plugin-help-please?replies=4#post-4548291
I was able to place everything behind the popup, but after you close the popup it hides the menu which isn't good either.
I even went into the css on the plugin and it should sit on top of everything, but it doesn't.
If you have a z-index of 100 on the box sheet as described above, the popup shows as it should, but when you close the popup, then menu is not functional.
So I tried several combinations to get things to work. But to no avail.
I would sincerely try a different popup plugin or build one from scratch.
Sorry
Tim"
Where do I go from here? The plugin works fine with Wordpress Twenty Eleven but then I lose all of the work that has gone into creating this nice theme.
I would really like to use this theme, please help if you can.