It sounds like you have some wonderful information to start with on your Great grandmother Margaret! Do you know where in Kilkenny she was born? This may give you parish/church information as before 1864, all records would have been kept in the locality. This would hopefully give you an idea of where to search for Martin and Mary.Rothe House
in Kilkenny has a genealogy department that can undertake searches, there is a cost involved but this may help with your searches.Kilkenny Library
is another source of records, again give their website a try and see if it can gleam some new information.
Hopefully, some of our fellow members and industry partners may be able to help too!
Have you been over to County Kilkenny yourself?