I think your best route forward would be to order a marriage certificate for William, which would give his father's name. I see from the census that Mary Jane was born in Liverpool, and also the children. It is most likely William went to Liverpool for work, as he seems to be in good jobs in the census details, and it is also likely that he married there. On www.freebmd.org.uk I can see a couple of possibe marriages of William Hughes to Mary Jane, Daniels in1873, Roberts in 1875 (this one was after the birth of the first child though). You can order the birth certificate online for one of their children to be sure of Mary Jane's maiden name. ( www.gro.gov.uk )It costs £7 for each certificate. You will need to get the reference numbers and places from freebmd first to place your order.
I apologise if you have already done all this and I am stating the obvious.
Good luck
Susan