No, I wouldn't say John & Eliza were James' parents because they were living in different houses. Perhaps Eliza was a widow?
If you can find the marriages of Christopher & James in the USA, and their father's are the same (or a family name), it might be a start to narrowing down their parentage.
I would also recommend finding every record you can for them in the States, as perhaps 1 of them may state a definite place of birth in Kildare and/or parents names.
At least you're lucky that the name is not Murphy!!