As you already know Thomas was born before Civil Registration so he doesn't have a birth cert.
You have already searched for him on RootsIreland with no result, they are still adding to their records so it may be worth trying again every so often.
You found a church record for Thomas and Ellen's marriage is that correct? 25 July 1867 but no parents named on it.
But it's not showing in the Civil Reg on FamilySearch.
As I see it your choices are,
A. Go to Dublin and search the GRO indexes yourself.
B. Go to Dublin and search the parish records in the National Library
C. Hope Irish Genealogy get their Civil Records back and maybe get the marriage there.
http://www.irishgenealogy.ie/en/D. Hope the parish records in the National Library go online someday.
but you may have to accept the records simply don't exist, which is often the case for these dates.
Did you keep in contact with ForeverEnding from this thread
http://www.rootschat.com/forum/index.php?topic=438381.9might be worth finding out if he found anything since.
Good Luck.