Wilma
This is just some speculation from me
As you have found, there doesn't seem to be a marriage for a John Gordon and Isabella (or variants) McDonald, parents to your James, or none that has been found so far.
Concentrating on Cabrach, I found this birth entry:
ISABELLA MC DONALD OR GORDON Birth: 18 MAY 1869 Cabrach, Aberdeen
Parents:JOHN MC DONALD and ELIZABETH GORDON
I also found this entry in 1881:
Elizabeth Gordon 77, Annuitant, b. Cromdal, Morayshire
Elizabeth Gordon 46, daughter, General Servant, Domestic, b. Cabrach
Isabella McDonald 11, granddaughter, b. Cabrach
Address: Gaugh, Cabrach
I am guessing this young Isabella is the one showing as born in 1869. I am also guessing that this Isabella may be James' mother. The young grandson James who shows in 1901 with his grandmother Beattrie Gordon at Gaugh, I wonder if her name is actually a version of Elizabeth such as Betsie or something similar (there's no such name as Beatrie and nothing showing for a Beat* in previous censuses).
And there is this 1891 entry that seems to help confirm that - everyone born Cabrach:
John Gordon 76, farmer
Betsy Gordon 61, sister
Elsie Gordon 16, niece
Jane Gordon 18, niece
Address: D(C?)augh, Cabrach.
The only way of confirming any of this, will be James' birth cert of course
Monica