I finally sat down and read cover-to-cover Dobson's Books 
looking for any other mention of the Loyalty besides our
Alexander in 1698. 

Carnegie, James
Indentured servant from Scotland to East New Jersey 
on the "Thomas and Benjamin," T. Pearson, November 1684

Carnegie, John
Aberdeen. Indentured servant for Virginia via Liverpool 
on the Loyalty, H. Brown, August 1698.

Carnegie, John
Educated Glasgow University. Episcopalian minister 
of St. Stephen's Va. 1702-1708. Died 1709.

Jean, do you know which church specifically our Wayman 
was married in ?

source - Directory of Scottish Settlers in North America 
1625-1825, Dobson. Genealogical Publishing, Baltimore.

Article here about ship speed across the Atlantic.