Hi again!

Is it possible that Thomas Jones was already married, and that's why they didn't marry sooner?

It might be worth investigating a baptism/christening record for Kate, if you haven't got one already. Usually, they would put something like 'reputed father (insert name here).' If they were illegitimate. What does Eliza put herself down on the birth certificate, does she put Eliza Hayes nee Clifford? Also, what is Thomas' occupation? Maybe there really was a Thomas Hayes?

It is rather confusing, I agree. Her father isn't Job, I think we can rule that out? Do you have his death certificate? It might be worth getting Eliza and Thomas' marriage certificate, if you haven't already.