Who were they?

Old Calton Hill Cemetery in Edinburgh has some noteworthy graves and memorials and probably my favourite one which is often missed due to its location is one dated 1756.  It was erected by Captain John Gray in memory of his parents.
 
It …   is in excellent condition, and is arguably the most interesting in the whole burial ground. It is inscribed with his name and then a carved anchor, beneath which is a carving of a 3-masted ship, flying the ensign, shown in bold relief. Down the left side of the stone is a skull and bearded, male head wearing a cap (his father). From the mouth spill two ribbons, that link symbols of death: a scythe crossed with another implement (not recognisable) and crossed bones. Down the right side is a female head, wearing a bonnet (his mother). Ribbons from the bonnet link again to symbols of death: a spade crossed with a coffin, and again crossed bones (specifically thigh bones).
 
I have tried to copy the inscription;

Captain JOHN GRAY.
Ordered this stone to be erected to the memory of his parents
ELISABETH WILKIE
who died Feb 3rd 1747 aged 67
also
THOMAS GRAY
Wright in the Pleasances
who died May 3rd 1752 aged 86
whose Bodies ly here interrd .
also
MICHAEL SWAN
who died 1746 aged 6 months
and
JOHN SWAN
who died in 1746 aged 9 years
both sons to JAMES SWAN
 
I’d like to know the relationship to James Swan and why the two young boys died within a short while of each other.   Also I wonder where John Gray himself is buried.

(Gravestone 1)