1. Can you pull up each MFD as a separate panel? My idea is to use my TS and drag an MFD onto it as I can do with the GPS.
Yes, but you have to modify the panel.cfg by yourself, adding a new 2D window for the MFD. Look the Microsoft FSX SDK, under the "Panel and Gauges SDK", the "Panel Configuration Files.html" document.
Note, the MFD are the only gauges that can be moved to a separate 2D screen, and you will only get the screen area, not the buttons, because those are 3D objects, part of the airplane model.
2. Are there key commands to activate all the controls used in the MFD's.
That would be quite difficult to achieve, since the F/A-18 MFD buttons are 3x20 = 60 separate keystrokes, so we had to use custom events, because there was no chance to get 60 available keystrokes from FSX. In theory, it should be possible to generate these custom events, because I think FSX handles these events by means of Windows messages (WM_xxxxx codes). But you would need to write some kind of Windows application that will generate these events, in response to what you touch on the screen.
