I have just today found my own link to the Allen's of Calloway County Ky.
I believe you should look to the name Rufus as the possible father of your John E Allen. I don't have access to the 1900 Calloway County Census. Neither does the library in Calloway Co. Rufus was the youngest of Hile Allen's children. Rufus was 11 in 1870, so this makes him a candidate. Good luck!