Hi Maureen,
With due respects to TFHF, and apologies to all if I have this wrong, but the service they offer is
"based on access to the Baptismal and Marriage records of the Catholic Church in the Archdiocese of Cashel & Emly".The Johanna Doyle b.1876 is almost certainly not the same Johanna b.Sept 1875 unless the TFHR record is mis-transcribed.
The BRS site lists a Civil Birth for Johanna b. 1876. As BRS don't have access to Cashel & Emly Church Records the fact they list the Civil Birth is a possible indication that she was in the C&E Archdiocese.
Personally, when consulting Church Records I prefer to go to the NLI which has the added bonus of giving free access but I realise this is not an option for everyone, especially those living outside Ireland.
Regarding John, is there an indication of whether he was still alive on the 1883 Marriage Cert? There is a death in Waterford that might indicate the family moved there before John's death:
Name: John Doyle
Registration district: Youghal
Record type: DEATHS
Registration date - quarter and year: Oct - Dec 1884
Estimated birth year: 1834
Age: 50
Volume: 4
Page: 605
As an aside, the OSI map at
http://ims0.osiemaps.ie/website/publicviewer/main.aspx#V1,607375,640394,6shows Boherclogh at the time you are researching. (Select Historic view).
Dara.