Perfs are almost identical but your ROI will be much better with Ubuntu as it's a free OS. I assume you won't run Windows without a license. Personally I prefer Linux as it's much more easy to setup and configure and works without maintenance. It's also easy to script. Use Ubuntu 14.04.
Yes you can mix non crossfire and crossfire cards. Just take care to have all cards ships of the same founder. Don't mix AMD and nvidia cards, you would have problems with drivers.
Booting on one of the mining cards it ok. If you use Linux, it doesn't impact performances if you don't run 3D things while you mine. I don't know about Windows.
You can run VM as it mostly use the CPU and mining is more on the GPU but be aware that anything will heat instead of just GPUs, so you'd better have a very good cooling system.