The book "Civil War Battle Flags of the Union Army and Order of Battle" by General C. McKeever, has many of the details you seek including the 9th Corps HQ flag issued on their way to Vicksburg.

There are articles in Military Collector and Historian by the late Howard Madaus that cover the McClellan system of flags at the later system (Butterfield I think?) that should also prove helpful to you/

The McKeever book was reprinted a number of years ago and will be easy to find.

I agree that the flag with Wilcox seems weird - more like the Second Division's flag.

Greg Biggs