Catherine d. Saint John 19MAR1849 and was a member of the Baptist Church. In theory, at least, they had been living in Saint John since at least 1807 (John S. Clark was initiated into the Freemasons in NB in 1806), and John was a deacon of the Baptist Church. He d. Saint John 21JAN1867. I would check the probate records for Saint John Co. for the relevant dates and also the baptismal register of the Baptist Church in Carleton Parish.
Daniel W. Clark was also a deacon, and his daughter was married by the Pastor of the Free Baptist Church, Carleton. This should give a fairly specific direction as to which church to search. The baptismal records of Yarmouth, NS should also be searched.
I suspect, considering the difficulties regarding census returns (being, early one, missing in Saint John and head-of-household in NS) that you only likely documentation will be probate records or baptismal records. Baptismal records in NB should be considered (including Anglican records) as, although Daniel in consistently given as b. NS, it seems that his family may have lived in Saint John or Kings Co., NB before he was born. Especially I would examine: "Baptist Records Saint John: Germain Street, 1810-1970", on microfilms F8821 to F8823 at the PANB.
See:
http://archives.gnb.ca/Documents/CountyGuides/StJohn_en-CA.p...for information on probate records in Saint John Co., especially Probate Court Book:
1867-1875 Vols. L, M F1343.
There is one piece of evidence than can be pursued. Dan Johnson's collection has at:
http://archives.gnb.ca/Search/NewspaperVitalStats/Details.as...m. Carleton, Thursday last, by Rev. F. Coster, James STACKHOUSE / Ann Wetmore CLARK 2nd d/o John S. CLARK. NBC CG NBRG
Also, at:
http://archives.gnb.ca/Search/NewspaperVitalStats/Details.as...The death is announced today of James STACKHOUSE, Esq., a life time resident of Carleton (St. John) and a descendent of one of the early settlers. Mr. Stackhouse has been an invalid for some years, but in his active days carried on extensive contract work, both by him and in connection with D.W. CLARK. He leaves a wife and six children, all we believe living here, except one, Mrs. SHARP who resides in England.
Also:
http://archives.gnb.ca/Search/NewspaperVitalStats/Details.as...The funeral of Mrs. James STACKHOUSE took place yesterday afternoon from her son's residence, corner of King and Ludlow Streets, Carleton (St. John) The services at the house were conducted by Rev. Cahill, assisted by Rev. Hickson and the same gentlemen officiated at the grave in the Old Burial Ground. Mrs. Stackhouse was a d/o late John S. CLARKE and the only surviving sister of D.W. CLARK.
So it seems very likely that you have Daniel's parents.
Thomas.