'John the Conquerer root' is said to be Ipomoea jalapa, a plant related to the large plant family which includes bindweed, morning glory and sweet potato. It may also be something else.

The "John the Conquerer," the prince who became a slave, and is invoked by the root, who appears in folk tales, may be mythical.

"red marks around a black slave's ankles"- authority for this questionable statement? Any mention of this with regard to prisoners who were shackled?

"Johnny Cuckoo" was sung by Joan Baez at Newport, 1963-1965. I doubt any relation of this song to the mojo weed. Baez probably got it from the Smithsonian or North Carolina collections.
It is the same song as sung in the Lomax-Bess Hawes albums. An excellent version by Janie Hunter from the Sea Islands (Johns Island, South Carolina) where it was associated with a ring song. See The Southern Folklife Collection, Louis Round Wilson Special Collections Library, University of North Carolina:
Carawan Coll
This is a very extensive and important collection of both Black and White materials.

Janie Hunter sings "Johnny Cuckoo" on the Smithsonian Folkways album, "Been in the Storm So Long," a Johns Island collection.
The old Carawan album of the same name has become hard to get.

There is another old song with Johnny Cuckoo, probably unrelated, called "Mulberry Hill," in which an old lady is making her will. Two couplets-

And there she sat down to make her will,
Aha, aha, to make her will.

The old grey mare to Johnny Cuckoo,
Aha, aha, to Johnny Cuckoo.

Library of Congress, Folk Songs of America: The Robert Winslow Gordon Collection, 1922-1932.
http://www.loc.gov/folklife/Gordon/sideBbandB5.html