Hi,
I have looked at the marriage cert for John O'DONNELL and Emma Ann NUTTY, 5 Jun 1878 Emma was 21 a spinster father William John NUTTY a carpenter. She lists in the census as born in Wells Somerset so yes I agree, you have the correct person. John was a soldier at the time of marriage and lists as being in the Army Service Corps in 1881, 1891 and still a barracks lab in 1901 so he was a career soldier. Naming his daughter Eileen Pretoria, I wonder if he was involved in the Boer War when Pretoria surrendered in 1900 - the name certainly had meaning to him anyway, hence his daughters name in that particular year. The name Pretoria was used in a lot of names in 1900.
I wouldn't be too concerned about Emmeline instead of Emma Ann. Emmeline is really just another version of Emma. (sounds a bit more classy) Also could you have wrongly read Emma Ann as Emmeline? Easily done.
I am sorry I have no military expertise to help with John's career. Someone on the armed forces board may be able to help further with that. All the best.
Cheers Kris
