You say you think John's parents are James and Naomi, since you know when and where John died, have you had a chance to obtain a copy of his death certificate?It should show the names of both of his parents, including his mother's maiden name.
1860 census Walker Co, AL:
McDonald, James, 61, b TN " Meorna, 57, b TN (handwriting not clear) " James A., 21, b AL " George W., 18, b AL " John R., 15, b AL
I do not have access to online 1850 census.The archived section of the Walker Co, AL GenWeb project shows there are McDonalds on the 1850 census index.
Have you checked land records for Walker Co, AL?See if your John shows up as an heir when the land is finally sold.