By now you may have cracked this problem -- I hope so! But in case not . . .
You refer (on 22 November 2009) to the first known man in your line being a William Brander (1786-1854), whose son James was born in the Azores in 1837 and was father in turn to the John (b. Azores 1857) who became your great grandfather. You add that "the family were Fruit Merchants based in the Azores but possibly originally from Elgin". And in your opening post you say that from your investigations up to that date you had found that "the family seem to be merchants and James at one point is named as being in Lisbon".
I wonder what the evidence shows about the activities of James (b.1837) in Lisbon. You do not specifically mention the James Brander who flourished there between ca. 1760 and 1780, though you may still know all about him. But it is always dangerous to make such assumptions, so: the IGI shows two local marriages for him, plus a number of children's baptisms -- though unfortunately they do not include a William. Perhaps further research could eventually reveal that one of the older ones produced a son of that name.
The interesting point here is that you stated that your Azores Branders were fruit merchants -- and this James Brander (in tandem with his brother Alexander handling the London end of the business) made his fortune in the citrus trade. As you may know, the proceeds allowed both brothers to buy a fair few acres near Elgin, and James went on to build himself an attractive house there named Pitgaveny. Country Life magazine printed an interesting illustrated article about the house and its owners on 23 August 2001 (vol.195, no.34, pp.52-57), which confirms as much:
"James Brander, who built Pitgaveny, was a self-made man. Born in Moray in about 1731, he made his fortune in Lisbon shipping oranges and lemons to London, where they were sold by his elder brother, Alexander Brander ... " (p.52).
There is also some material about this family accessible via Google Books, in vol. 1 of Burke's LG 1847 -- though what is shown there is in part contradicted by the evidence visible in the IGI.
Rather more speculative material appears in the IGI for Spain, which shows a baptism submitted by an LDS member (i.e. much less dependable than entries generated by the controlled Extraction Program). The parents are recorded as William Brander and Hester Dorothy Burnett, and the child was christened Robert Burnett Brander. The entry was been submitted four times: all the entries say that the birth occurred at Malaga on 6 November, though they disagree about the year: three give 1795 and one gives 1793. Both dates are obviously too early for the father to be your William. But any Iberian Branders naturally catch one's eye. Several daughters born in the same period are attributed to the same parents, all with Spanish forenames. One of the daughters is shown as dying in 1887, with the source apparently being an unnamed book held (?)at Salt Lake City.
You will no doubt also have considered (and it seems excluded?) the William Brander son of John Brander and Margaret Young, who was christened at Drainie in Moray on 14 February 1786 -- per the IGI. He and his siblings may perhaps have some connection with the people who built Pitgaveny and may even have been recruited into the family business, though I have not had the opportunity to explore further in that particular direction. Maybe someone else can help you there, if in fact you think that child could still be a realistic candidate.
At all events, it would be interesting to learn whether you have made any further progress since your last posting here.