At Fort Hays Days in Hays, KS, this Friday 9/12 at 7pm, there is going to be a presentation on the life of Tom Custer. The presenter, Roy Bird, is the author of the book, "In His Brothers Shadow: The Life of Thomas Ward Custer."
Perhaps it is possible Bird might be able to answer your question regarding a "Major Custer." If you can't make it to Hays, or if his book doesn't shed light on your question, you might try writing Bird at Washburn University in Topeka where he is an adjunct professor.