Thank you for your reply and for all the new leads. I had heard that he had 2 illegitimate children so perhaps Agnes is one of them in which case her mother could be the Mary on the marriage certificate but I can't find any paperwork for either of them. There is a letter that another researcher owns where a contemporary of Benjamin b.1861 (the bridegroom) says that 'Ben has just married his cousin from Australia and is now wealthy', she brought £500 a year to the marriage. Agnes and Benjamin went on to have 3 children in Scotland before disappearing from the records after 1891 census. I know that he got thrown out of his job in about 1894 and know nothing after that.
This is so confusing but i will now follow up all your leads and see where they take me. I think I need to look at passenger lists from Australia to Scotland around the time of the wedding and take it from there.