Mary Ann's death record(1907) does not show her parent's names
Here is the family in 1861 census which you said you did not have - they are indexed as Shippy
1861 GRIMSBY,LINCOLN, CANADA WEST SHIPPY
Samuel age 36, labourer
Mary, age 36
James, age 12
Margaret, age 10
Sarah, age 6
Isaac, age 1
Helen, age 4
** all shown as born Canada West ** so no Charles who according to marriage was born about 1852
familysearch.org has a death of a Margaret Jane ROUGH who is daughter of Samuel Shepherd and Mary Ann. This Margaret born about 1852Upper Canada - so looks very possible as daughter of your Samuel. She is listed as married, age 23 years, 7 m months, 23 days, housekeeper - died April 22, 1875, Volinia, Cass Co. MI. She died of Inflamation Both her parents shown as born residing Upper Canada
I looked at the image for this death and on same page is a Harry J. ROUGHdied Sept. 16, 1875 , age 5 months 5 days, born Michigan Parents William W. ROUGH and Margaret Jane - residence Michigan
There is also a birth for Harry J., born April 11, 1875so Margaret died not long after his birth.Harry's birth shows parents William W. ROUGH and Margaret Jane. Wm. born PA, Margaret born Upper Canada. Wm. is a shoemaker I have not been able to find amarriage for Wm. and Margaret, nor any other children.
Did you want me to look for children of James, Charles, Sarah, Hellen, Isaac, Anna and Ada ?