Here's the updated version of the atlas, with German and Russian rise areas fixed and spawn locations included for Persia, Japan, and the Mayans. Because the wiki doesn't allow easy updating/deleting of files I'll just post it here in the forums and provide a link to here from the wiki.
In addition, the zip files contains a directory called bonus_files, which are map overlays of the civ "normal areas" which I needed to figure out for victory conditions anyway and Continents.png which is a sketch out of the continents as provided by Rhye in this thread a little back. This later was mostly for my own curiosity, as I'm playing Russia right now and was perplexed by the Europe/Asia boundary. The normal areas are used (I guess) for some stability calculations and for resurrection/rebirth of civs.
I'm not including these files in the normal interface right now, but they are there for the curious to download. You can overlay them using the "Local Files" box by specifying the full path to the file on your local machine and clicking the check box. I don't guarantee the accuracy of these bonus files, since I didn't double-check them (and look how many mistakes I made on the files I did double-check!).