Thank you both for your responses.
I had found both Francis Johnston and John Johnston in Griffiths. I know that my Francis William Johnston came from Muckross, Fermanagh, from info on headstone inscription of FWJ in NSW - it is written there with 2x's'. I know Griffith's uses one 's' but I have seen it spelled both ways and I've continued that tradition.
Given the small size of Muckros, I figured that it would be safe to assume that the Francis Johnston mentioned in Griffith's was indeed father to my two chaps.
My chaps were Protestant after arriving in Oz so I assume that the family remaining in Ireland would have also have been Protestant.
From his DC and MC, I have calculated that Francis William Johnston who moved to NSW would have been born circa 1835.
I don't know of the birth year of James - he seems to have kept a very low profile and I'm still working on him. As you'd both know if you have an interest in the Jonston's you'd know how common their names are - I have at least 3 James Johnstons in NSW who could be the one's I'm trying to confirm. Francis and James had a cousin who also came to Oz called Gerrard Irvine (again very common in all generations of my family since the mid 1800s).
Do either of you have a Johnston connection/interest?