1 - I don't want MC-16 to just go off and try to discover files - can I control this?
Yes, turn off Auto Import. Tools/Options/Library & Folders and uncheck "Run auto-import in background"
2 - Can I import my history (especially last play and play count) from FB2k?
I don't know.
3- While your import is running, my desktop is in repaint HELL - can this be fixed?
I have never experienced this.
4- Do you have Kernel Streaming?
Yes, Tools/Options/Audio then choose Kernal Streaming under Output mode
5 - Can I run multiple instances of MC-16 - One for Audio, and 2 for my dual monitors for video?
Yes, Tools/Options/General scroll to the bottom and expand "Advanced" and check "Allow multiple instances to run at one time"
6 - If so, can the instances be set to use different audio system (main, desktop etc)?
I am not sure about this, but you could use zones to achieve this.