Mystery solved.

In 1891 have an Emily Quilliam as a border in Patrick with William and Margaret Callan at Ballacallan.
There is also a widowed Elizabeth Quilliam 87 at this abode! She is described as Mother.
If she is William's father, it could be by a different father than James's father.

I found Louisa, Emily and Catherine Ann in Leeds in 1901. Catherine Ann 29 is married to Thomas Frederick Elwick 31 a carpenter and joiner. Emily 21 is married to Arthur Elwick 21, also a carpenter and joiner. Louisa 24 is Married to John Dicki(e)nson 27 currier (leather).
They all married in Leeds. The marriage certificates will give the father's name and profession. The reference for Catherine is June 1893 quarter Leeds Vol 9b page 587, for Emily it is December 1900 quarter Leeds Vol 9b page 942, and for Louisa it is March 1901 quarter, Leeds Vol 9b page 663.
New mystery: who is this Elizabeth Quilliam in 1891?