You probably already have this but I checked Thom's 1863 for the address :
Grattan place (off Grattan Street)
1 tenements
2 Thos. James Walsh, cook & confectr.
4. Mr. John Horan G.P.O
5-6. tenements
7 Mr. John Forde
8-22 tenements
One possibility for further research would be to track any records you can find for Martin families in the parish, and gradually build them into separate family lines. That way when you find possible members you can check where they fit to see if they are your Martins or not.
One problem you may find with RC records is that they dont usually mention a persons occupation, which might have been useful to check any possible various John Martins.
I'd say the best way to do this is to use the website at
http://www.irishgenealogy.ie/ They are adding more RC records for Dublin city later in the year.
Do you know when father John died ? Even though death certs dont contain much information If he died 1864 or later it might be worth searching for one.
p.s. one more possible (very) long shot - if the family were involved in some newsworthy event, legal (or criminal) matter, they may be mentioned in a news article. If this is the case, an item probably would not give much family detail, as it could refer to people as 'Mr. Martin of ..zzz address etc. It might be worth a try...The Irish Times started publishing in 1859, and other newspapers were being published at the time - e.g. Freemans Journal. (both are available on subscriptions websites)
Shane