Q:

How to digitize polygons from georeferenced raster file

I used QGIS to georeference a raster file of a custom US map.  The map has features which are not strictly defined by state borders.  I would like to digitize the map by creating contiguous borders for each feature.  I tried that a few different way, but none of them really worked:

traced the borders with polylines, and digitizing with the Polygonizer plugin.  The plugin kept crashing. 
used Conversion > Raster > Vectorize (Raster to Vector).  That one worked, but the result was many overlapping polygons for each feature, each with slightly different borders. 

I have somewhere between 50-100 different raster images to process, which is why any automated solution is highly preferred.  I'm new to GIS software, but could easily pre-process the images if needed, either manually or with a custom script (using Python/PIL, ImageMagick, Photoshop batch processing or similar tools). 
Thanks for any pointers! 
Original

Georeferenced image

A:

What you could do is:

In the original image, fill each area with a unique color, e.g. with Gimp
Georeference 
Run Raster to Vector
Clean up the polygon geometries manually

