Some updates:
I figured out how to do a fast resize, so I'm using that to improve speed rather than line skipping, you'll now see an 'Analysis Size' option, this is the size in pixels to shrink the longest side down to. Default is 200, you might get away with 100, it's pretty fast.
You can specify a crop for the histogram analysis. You just have to enter x,y,width,height (in percent), no way to allow you to draw it with some sort of UI, but the preview will draw the crop box so at least you can see where it is.
You specify max iterations, rather than iterations, the script wont do another iteration if it thinks it doesn't need to (the histograms are already as close as it can make them). If the script thinks there is still potential room for improvement after max iterations have been reached, it will popup a message box indicating this.