I also have a feeling that flag was, or derived from some militia patterns of VA's flag (that's the connection I am trying to prove). Not quite sure what info I am looking for on the OOB link that you posted. I am familiar with that site since I created it and used to be it's webmaster. The 47th and Barton's Brigade of VA regiments were on a different sector of the field, and while they all may have lost colors (if they still had any to lose), they did not engage against any of Custer's men. Wise's men if I'm not mistaken (at first glance) appear to be in the correct sector of the field, which is why I need to look at them a bit more, and at the ORs for all of Custer's regiments.
Josh Bucchioni