1871 Canada Census for Freeport, Digby Co, NS:
FOOT, Samuel FP 40m - - ship capt.
Lizzie 38m - -
Edward 14 -
Samuel 2 -
ELLIS, Charles 19 - - seaman
Edwin 14 - -
Edward or Edwin??? Seems if he was a FOOTE by birth, he was s/o Samuel and Lizzie. He may have been adopted, or just adopted the Foot/Foote name later in life?
Surely, if he was an Ellis, he was brother to Charles - hard to say.
Samuel (Jr.), b. @1869, was living with John and Elizabeth Smith and family in 1881, at Tiverton, in Digby Co., NS.
The Lizzie married to John Smith was Lizzie A. Foote (widow of Samuel), in 1880.
Samuel Foote was b. 08-Jan-1869, Freeport, s/o Samuel Foote and Susan Ellis.
Suspect Susan must have been related to the Charles and Edwin shown in 1871 census at Freeport.
Samuel and Susan were married 1856, Long Island (Freeport), Digby Co, NS.
Samuel Ellis Foote m. 19-Dec-1908 at Freeport, to Theodora May Perry. He was 39, she was 26.
His parents were listed as Samuel and Elizabeth.
Interestingly, on Samuel Foote's 1955 death record, instead of parents being listed, that part of the form is filled with "Adopted Child".
Further digging shows Susan (Ellis) Foote d. 19-Dec-1869, at Freeport, 11 months after Samuel Foote was born.
Susan ELLIS Foote was 36 when she died in 1869, born Yarmouth, NS, d/o Samuel and Susan ELLIS.
The Elizabeth who later married Samuel and then John A. Smith, was b. @1831, in Kempton/Kimpton, NS, and was the d/o Thomas and Susanna.
SO, though a bit of a mess, maybe with other clues in your possession already, the above may prove in some way useful.