So far as the May, 1862 wool/cotton issues with 12 stars - and this is off the top of my head - the following flags remain:

25th Virginia (MOC I believe - captured at Gettysburg)
31st Virginia (Richmond UDC)
5th Alabama Battalion (attributed) (ADAH)
18th Georgia Infantry (private collection)
unknown unit captured in the Wilderness (possibly MOC)
1st Maryland Cavalry (New York Military Museum)
12th Georgia Infantry (Columbus Museum)
1st Texas Infantry (Texas State Archives - Sharpsburg capture)

There may be a few more. These flags were issued to Hood's Brigade, Elzey's Brigade and Steuart's Brigade and 20 of them went to Jackson's Valley Army according to a soldier of the 12th Georgia.

Greg Biggs