So far as I know, Milligan had no connection with the Mormon Church, but he was a maverick in his field because he believed more of the ancient American peoples came from the south, probably by sea, and moved northward rather than migrated over the Bearing Strait land bridge as is more popular in the field.
Most compelling about Ed's theory was not the ancient legends which collaborated it, but the observable fact that the level of ancient civilization decreased rather than increased when moving south to north. If the Bearing Straight theory was such an ironclad fact, then we ought to have ruins along the coast of say, modern day British Columbia which rival those of the Inca in Peru.