In Tableau Version 8, it will be possible to insert parameters dynamically into Custom SQL in order to bring back specific subsets of information. Whether or not it will solve the your specific data problem, I cannot know; it will certainly be something to look into regardless.
As of right, your best bet would be to create the extract and then have an Action that just filters down to that one store. A 50+ million row extract is not a problem within Tableau. It may take a bit of time to create, but once it is done you should be able to dynamically switch between stores on your map to get the desired information.
Hope this helps,