I may have found James Thomas on the 1871 Wales Census...
According to his marriage certificate (1878), he was residing in Neath at the time, according to the 1881 Wales Census, he was born in Cardiff..
So:
Might this be him in the 1871 Census?
Name: James Thomas
Age: 19
Estimated Birth Year: abt 1852
Relation: Lodger
Gender: Male
Where born: Cardiff, Glamorganshire, Wales
Civil Parish: Neath
Ecclesiastical parish: Neath
Town: Neath
County/Island: Glamorgan
Country: Wales
Registration district: Neath
Sub-registration district: Neath
ED, institution, or vessel: 21
Household schedule number: 9
Piece: 5430
Folio: 53
Page Number: 2
Household Members:
Name Age
Jane Thomas 35
Jane Thomas 15
John Thomas 11
Mary Thomas 5
Thomas Thomas 2
Ephram Jenkins 21
James Thomas 19
In which case, perhaps the elder Jane Thomas is John Thomas' sister? Not sure if that helps us any.