Lots of theorizing here, especially trying to explain Ballygran/Ballygrot, 'marble stones,' and Kilkenny's anomalous presence in the song. But it all makes sense if you start with a visit to Google Earth! If you look at geography, the 'mysteries' of 'Carrickfergus' are really simple and quite straightforward.

Carrickfergus is a port on the north Irish Sea. Ballygrant is a village across the Irish Sea on Islay in the Inner Hebrides of Scotland. It is about a day's sail north from Carrickfergus. Less than a mile from Ballygrant is the parish church and burial ground of Kilmeny. You can find these sites on Google Earth, and note their proximity.

Given the vague oral tradition of the song, Kilkenny is likely a mis-hearing on O'Toole's part. In both time and distance, Kilkenny is much, much farther from Carrickfergus than Kilmeny, and has no association with a place called Ballygrant. Nor is Kilkenny anywhere near the sea. So let's apply Occam's Razor to the song, and go for the simplest explanation:

'Carrickfergus' is simply the song of a man and his memories of a love across the sea at Ballygrant in Islay - a love now deceased and recorded on a 'marble stone as black as ink' in the burial ground at Kilmeny.

Here's my guess as to what the lyrics to Carrickfergus should be like:

                I
I wish I was in Carrickfergus,   
Only for nights in Ballygrant.
I would swim over the deepest ocean
To lie beside her, in Ballygrant.
But the sea is wide, I cannot swim over,
And neither have I wings to fly.
If I could find me a handy boatman,
I'd ferry me over to my love, and die.

                II
My childhood days, bring back sad reflections
Of happy times spent so long ago.
My boyhood friends and my own relations
Have all passed on now, like melting snow.
So I spend my days in endless roaming.
Soft is the grass, and my bed is free.
Ah, to be back now, in Carrickfergus,
On that long road down to the shining sea.

                III
Now in Kilmeny, she is recorded
On a marble stone there, as black as ink.
With gold and silver, I did support her.
But I'll sing no more now 'til I have a drink.
I'm drunk today, and I'm seldom sober,
A lonesome rover from town to town.
Ah, but I'm sick now, and my days are numbered.
So come all you young men, and lay me down.

-- Jack Maloney --