Isolated to deal with the problems sequentially and specifically.
http://www.whipplephoto.com/Genealogy/getperson.php?personID=I17076...
Problems begin *right at the top* - those "parents" are NOT POSSIBLE.
Thomas Wilson
Birth 1638 Killybegs, County Donegal, Ulster, Ireland
Christening 16 Sep 1641 Torryburn, Fifeshire, Scotland
Uhh...NO, that's too long after birth and too far away from birth place.
Marriage 7 Jul 1663 Dunfermline, Fifeshire, Scotland (Margaret Donald) MARK THAT DATE!
Children
1. Adam Wilson, b. 10 May 1664, Dunfermline, Fifeshire, Scotland (ok)
2. Ephraim Wilson, b. 2 Dec 1664, Killybegs, County Donegal, Ulster, Ireland - NO WAY! Do the Math!)
3. Margaret Wilson, b. 21 Mar 1665, Dunfermline, Fifeshire, Scotland (NO WAY! Do the Math)
4-10 all born Dunfermline, Fifeshire, Scotland
Ephraim sticks out on this tree like the proverbial sore thumb - born 7 months after his "brother", 3 months before his "sister", and clear across the Irish Sea from *all* his so-called siblings.
You can't even fudge Margaret by claiming her birth date is 1665/6, because her sister Agnes is born in 1666!
So no, Ephraim blatantly DOES NOT BELONG to this family.
(Rev. Thomas' parents area also problematical, and look suspiciously like a snatch-and-grab.)