Re the mouse scale, it seems like the scaled mouse location and the area available for input are handled differently:
When viewable area is 75% scale of game display mode:
mouse scale=1.33 makes the mouse pos correct in game, but right and bottom 25% of window wont accept input
mouse scale=.75 makes mouse pos incorrect in game, but available input area is entire window
Re the character screen window, I saw the On Window Position event and was going to do just what you said, only executing if viewable.x != display.x to prevent the loop. Then I got lazy and just ran a script at char select to fix the windows
These issues are minor to me, because I think IS is FREAKING AWESOME and you should receive some kind of geek award. I 5 boxed EQ back in 2000 and it was a major pain in the ass, mostly because only the foreground window could be visible or it would kill the system, and none could display on a secondary monitor. It was alt-tab hell (and for a while even that required hackery).
I was boxing WoW for a while recently and that is how I came to hear about IS, from those long nasty threads on dual-boxing. I have to give kudos to Zanthor for all the info he posted, between his scripts, the wiki, and the default IS script I've figured it all out pretty quickly. I'm back to EQ anyway, old school mmo is more fun for me.
Anyway, keep up the good work!