Easy way to 'draw' pause/exit screen in fp would be to take a screenshot using fplaunch, force fp to minimize and draw screenshot with pause overlaid (or exit options). From what I've read so far all of that can be done with ahk scripting, not sure what impact it'd have on resources though, and I know that ahk isn't the best at imaging (flickers a bit, especially when redrawing over a gui element) but all that can be worked around in the long term.
Yea, focus is an issue, I know what to fix, just need to be home to do it.
Also just realised that the new version of autohotkey has ansi and unicode builds, for our purposes the older ansi based style is going to be better, as that is the version bbb was using originally, and think that's the same for the HyperSpin ahk script.