John, I believe you have solved your own mystery about who John W. Allen belongs to. If Ephriam Allen and wife Patsy Skelton moved to Crawford Co., GA. at the same time as John W. and wife Elizabeth, then in my opinion, this seals it. Have you looked into Crawford Co. and Spalding Co. records?
In Joseph Allen's will, only the name John is mentioned. As I stated earlier, we know nothing of him beyond the will. No marriage record, nothing. And think about looking for the name "John Allen", sort of looking for "John Smith".
Hope you find some good evidence on your family. Please let me know what you find on Ephriam Allen. I am trying to put together all data on the Allens of Wilkes/Elbert Co.