It's worth bearing in mind that Civil Registration started in 1837 - so it's possible that Samuel's parents marriage, or the birth of any older siblings, would be in parish or nonconformist records. And there are cases where the church records continue after 1837.
And if you are still following the connection with Liverpool, have you considered that the Hugh Jones listed there is Samuel's brother? And that Samuel might not have been an orphan - he was old enough at 12 to have left school and joined the thousands of Welsh people who moved to Liverpool to find work. Younger people would normally be lodged with relatives.
Good luck - it's conundrums like this that keep me engrossed in this subject.
Alyn