Same problem here. Multi monitor support has some serious problems in Yosemite. The flickering/redrawing status menus issue is especially annoying with the UI in dark mode, so I've been forced to turn that off, but that hasn't alleviated the problem. But I ran into an even worse bug today. All the menus of the current app (except the main one that has the same name as the app) disappear every two or three keystrokes. They will then reappear a couple keystrokes later (or whenever I use a keyboard shortcut that triggers a menu command). So my entire menubar was flickering all day at work.
It's not every app that does it. Seems to only happen in apps that have at least one menu with an icon heading instead of text. Unfortunately, both BBEdit and Outlook have an AppleScript menu (the 'S' icon), and those are where I spend most of my day…typing!
Yosemite is running really smoothly on my iMac and MacBook Air at home, so it seemed safe to upgrade. Nope. Complete disaster for me. Now I can spend the weekend downgrading to Mavericks, then wonder how long it'll be before that machine can sync with other things over iCloud, since everything else is using iCloud Drive now. Awesome.
If you use multiple monitors, don't upgrade to Yosemite. That's the only solution until Apple fixes this half baked crap.