Mike,
You have obviously put a lot of research into this theory.
The flag in Iowa is no recently discovered artifact. Modern
flag researchers have known of this flag for almost forty years
now.
While your theory is well thought out; it cannot be substantiated.
There is no evidence of the flag in Iowa being anything other than
a nondescript South Carolina flag. It cannot be traced any further
than to the man who presented it to the Iowa Historical Society.
No connection can be established to Culpepper's Battery, the Citadel,
or even to Charleston.
No reference can be found concerning the flag flying over the Citadel
Cadets on Morris Island until the Civil War Centennial in the 1960's.
Then, and only then, does this flag become important.
Have you found any war-time letters, diaries, newspaper articles concerning
this flag? Have any post-war memoirs been discovered that herald this flag?

Ken