Hello Antaares,
Several years ago I came across this entry from The Census of the Parish of Kildress 1766, in County Tyrone. I saved it because of one of the other families in the list. It has a John McIlhone, Catholic, potentially the father of your John, and two other Catholic McIlhones. Also in the same townland there is a Miles McElhone, Catholic, and potentially of the same family.
Census of the Parish of Kildress 1766 in Co. Tyrone
Transcribed by Teena
LDS FILM 1279330
1766 RELIGIOUS CENSUS OF IRELAND
P = Protestant; C= Catholic; D = Dissenter
Townland - Beaghmore
George CAMPBELL C
Mick CAMPBELL C
Edward LYNCH C
Miles McELHONE C
John McILHONE C
Neal McILHONE C
Hugh McGERAGHTY C
PatrickMcILHONE C
Owen O'DONELLY C
Gilly O'LOCHRAN C
James O'LOCHRAN C
Lawrence O'LOCHRAN C
Cork O'MACKILL C
Arthur O'QUEEN C
Mathew O'QUEEN C
Mick O'QUEEN C
More recently I did a search for a friend for McElwains in Kildress Parish and found only one, a William McElwain, in the Tithe Applotment Book in Kildress Parish for 1826. He was Protestant and lived in Drumnaglough Townland about only 4 miles to the south-east of Beaghmore Townland.
My sense is that the variable spellings of apparently the same surname hasn't much to do with the family's English spelling preferences, but with the census takers choices. He interviews the people in Irish, their spoken tongue, and then reports the information in English, rendering the Irish name he was given phonetically into English. So manifold spellings of the same name.
Hope this is helpful,
Willim