I don't think your family came from Co. Kerry. Kelly and McDonagh are not surnames usually found in Co. Kerry.
I believe the records you located in Athenry are likely your family. The parish register for Athenry is badly organized at least in the early part of the 1860s. The Roots Ireland (subscription site) transcribers were also very confused. You can't tell if John and Catherine were married in February 2 1861 or July 2 1861 but I believe the February date is correct. The baptismal date is even more confusing as far as its placement on the register but I lean towards December 21 1861.
Unfortunately, the Athenry records start very late (1858). I searched for a John Kelly with the parents names you listed but no record came up. I searched for a Catherine McDonagh baptismal record in 1836 in Galway but no record came up.
Let me know if you have any questions.