Is there an easy way to pop up a window, and disable all click events for other windows and gameobjects?
I believe the short answer is 'no' and the (hopefully) best answer is 'not yet, but they're working on it'. This has been asked and answered here, please search on it. The general workaround is to detect that the mouse pointer is over a GUI element (I use the gui window containing my buttons et al), set a global boolean that indicates that the GUI is up and the mouse is over it, and then check that boolean in places where the mouse/keys would be otherwise used (MouseLook, FPSWalker, etc.), to return without doing anything.