Agree completely with your assessment that Willam Murray and Joanna Tupper from Sandwich, MA are not the same as William and Joanna Tupper from Milton/Liverpool Queens, NS.
The diary of Simeon Perkins, 1766-1780 which is searchable online here:
http://link.library.utoronto.ca/champlain/item_record.cfm?Id...Provides some clues.
There is frequent mention of a William Murray starting in the beginning of the diary in 1766 of a William Murray who has a sawmill and is a logger. Another prominent resident is Nathan Tupper and there are some Fords mentioned also.
Almost all the residents, 594 out of 623 are from the US so your Wm and Joanna may well have been born in the US, but they were living in Queens in the 1760's on through the 1780's based on the Perkins diary.
This seems like a much more promising line than the links to Wm and Joanna in Massachusetts, although William and Joanna could well be related to them.
To the extent that helps, here's my problem. :>)
I have a James Nickerson Murray Sr in St Mary's Bay, Digby married to a Hephzibah Doty a direct descendant of Edward Doty of Mayflower fame.
There is a second Murray, William, born one year later than James who also married a Doty along with an Albert who married a Doty. Albert is from Liverpool and his parents are David and Priscilla Murray which links the Digby and Liverpool/Milton Murrays.
Everyone has assumed David's wife Priscilla is a Nickerson, though there is no support for this other than other trees which also have no documentation for this.
But, it seems reasonable that James NICKERSON's mother was likely a Nickerson and there are Nickersons in Liverpool/Milton Queens County so that while there is no documentation, it seems a reasonable working assumption.
David and Priscilla were married in 1819, but the first children shown in the various trees are not born until 1832. I'm guessing that they in fact had at least two, James Nickerson 1824 and William 1825 who then moved to Digby County and maybe others between 1819 and 1824.
The early census data for St Mary's Bay is a mess. There are 16 pages in one with no surnames.
The other clue in all this is that the St Mary's Bay Murrays and Dotys were Baptists and among the 18 founding families of the only Baptist Church in the area. There are also some Nickersons on Long Island, just across the Bay from the Murrays and Dotys who were also Baptists so I would guess that if there are records of the Baptists in Milton/Liverpool linking the Murrays, Tuppers, Fords and Nickersons, that may help further clarify this.