Hi Monica and Nessie,
Sorry for the late reply, but I had been writing exams, so was a bit preoccupied. Thank you for all you assistance, the information that you have found is brilliant.
With regards to John Bennie's time at Glasgow University, it is mentioned in letters and reports of the Glasgow missionary society. It is possible that no record exists because he cut his studies short to move to Africa as a catechist.
The baptism information is enlightening as it confirms to me that the merchant James Bennie is almost certainly not John's father. The sponsors, John Scott and James Ramage, could be useful in tracking down a marriage for James and Margaret and their parents hopefully. although John being a common name, it might not help too much. I have found this in a quick search, although have not had time yet to verify anything in it, but there does seem to have been a James Ramage from Barony in Glasgow who was also a smith, and was born in 1770.
http://freepages.genealogy.rootsweb.ancestry.com/~cowiepatt/cpf1285.htmlSo he could possibly be someone who James worked with. and John Scott I would assume is likely a brother or father of Margaret.
Hopefully this will allow me to track down a bit more on James and Margaret,
Thanks again for all your trouble

It is very much appreciated.
Regards,
Duncan