I dont know what regiment captured Custer's HQ flag but it was recaptured at Sailor's Creek.
List of Confederate flags captured at Sailor's Creek:
40th Va--1st ny cav
76th Ga?--1st Wva cav (there was not a 76th Ga regiment)
18th FL--1st Wva Cav (there was not a 18th FL regiment)
27th Va--3rd Ind Cav
12th Va--2nd ny cav, 12th Va---1st Wva cav (2nd flag captured)
Sumpter HA---1st ny cav
9th Va----2nd ny cav
18th Va---2nd ny cav
8th FL----2nd Ohio Cav
26th Va---3rd Ind Cav
I will update this when I find more info.
The 61st Massachusetts one of the last Massachusetts regiments to take the field, guarded the Confederate Pow's from this battle.
Like usual feel free to add on or correct me.