Solution for the Click-Through problem
It's a known problem that clicking on a window will let the click fall through to anything underneath. This is most noticeable with mods, although it might also be endemic to some of the stock windows.
I released a fairly simple mod which solves the problem by providing a wrapper for the GUI.Window and GUILayout.Window calls, the link is below.
I don't know if this will be helpful, but if there was someway you could override the stock calls and use this, it would solve a lot of issues that people have with this.