Ok, now I get it.
If you accidentally undock the output window, you can redock it by dragging it over the main window and dropping it when the mouse cursor is on the bottom status bar of the main window.
But, if you can't find the output window at all, I'm not sure how you can deal with that. However, with some snooping and trial-and-error, I believe you can reset the window positions to their defaults by editing the settings/UserSettings.ini file and commenting out the "placement" item, e.g.
[Interface Settings\default\MainWindow]
#placement=2c 00 00 00 00 00 00 00 01 00 00 00 ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff ff 9c 00 00 00 9c 00 00 00 1c 05 00 00 ed 02 00 00
That worked for me after I dragged the output window off to another monitor (i.e. it put it back in the default position, along with the Find Results window). But you do have to use F8 to make it visible (as the default is turned off).
As for the "Individual Output Window", there is an option for that on the Project Tools dialog, but it isn't respected by the ASB compiler. (It didn't seem very useful to me to have separate output windows for every source file.)
Hopefully that will solve it with a little less effort than a full reinstall.