It's been an interesting day. :-) I think I've pretty much exhausted all the materials online, and have found the following:
1) James (Captain) Weems came to America in about 1695 as a soldier from Scotland. He never left and died in 1723 in New York. Children unknown.
2) The PA line of Thomas Scott Weems, father John Weems was born about 1673, but there is no record of him ever emigrating to the US. There is another John Weymss in the Darien records, but he went to Panama, and another who went to Georgia. If they "are" the same people, the Darien records give his origin (Canongate, Edinburg) and parents, Alexander Weymss and Bessie Innes. (Make note of the name Alexander.)
3) The only recorded child of John Weems and his wife Isabella Scott is Thomas Scott Weems, b. 1704. There could have been more - should have been more. Meaning John Weems was born about 1673 and could have been a son of Captain James Weems, and brother of James (Deputy Surveyor) Weems of Anne Arundel County, who is also unaccounted for. He doesn't belong to the AA group. Or he could be the John Wemyss that emigrated through Panama.
4) Thomas Scott Weems family was born and raised in Cecil Co., MD, a fair distance from Anne Arundel. "Both" John and Margaret fit in well to his family and he does have children named John and Margaret that are unaccounted for. No one's ever tried to connect them until I did. And, someone in your family did think that Margaret was born in Cecil County. Thomas Scott and his family all moved to Abbeville, SC which isn't far from the jumping off point of Hillsboro, NC. In fact, Hillsboro was the jumping off place for most everyone goes into the wilds.
5) There is another unaccounted for bunch of Weems in Sumner Co., TN (now Macon Co.,) that could be related to John and Margaret Weems. No one has ever done quantifiable research on them because they didn't seem to be part of the Anne Arundel crowd, where all the royal blood was.
6)There are two marriages in Boston, MA, one for Thomas and one for sister Hannah; 1717 and 1724, meaning they came from a family that was here before 1720.
7) There is also an Alexander Weymss, came to US in 1695 through the West Indies, same as James (Capt) Weems. Records say he settled in New York. Quite a coincidence?
I think what we've found is the remnants of Captain James Weems family. He obviously married and had children in NY and had family in Boston, where his wife (Anne Campbell) and her father lived while he was the 2-yr governor. They seem to have gone from NY to MA to PA, to MD in Cecil Co., MD. That's close enough to the Gott family for Margaret to have married a Gott family member. I think that Alexander could very well be a brother or relative. He came from Canongate, Edinburg, Scotland.
Tomorrow, I've going to finally make it to the library, where I've pulled their list of NY genealogy records and matched it against what is available at the NY City library. The Davenport library has many of the same books and has a great collection of early records. I should be able to find something. Will also check out the PA, MA and MD books as well.
In the meantime, I've ordered land record, title searches on the Weems tract in St. Mary's Co., MD in 1657, church records from MD, and will continue to search for evidence that John and Margaret Weems are either the children of Thomas Scott Weems, b. 1704 or additional information on the Boston and NY Weems.
We now have the following suspects:
James (Captain) Weems from Albany, NY b. abt 1660 d. 1723
Alexander Weymss from NY b. abt 1670
Thomas Weems, married in 1724 in Boston b. abt 1700
Thomas Scott Weems b. 1704 in Bucks Co., PA
and a bunch of renegades who poison their husbands in Sumner Co., TN. (long story!)
Hope your day went as well!