Sorry to get back to you so late. There are many descendents of Duncan Stewart here in the U.S. who have tried unsuccessfully to identify his family line in Scotland.
I have been to Edinburgh a number of times - The Stewart Society and the large library in town - and had no luck. I even hired a well known Scottish genealogist to search.
We know Duncan lived in Ipswich, Massachusetts as an indentured servant to one George Hadley. There were many prisoner from the Battles of Worcester and Dunbar who were sent to the Americas at that time but the ship's records are incomplete and we could find no evidence from the old English prisoner lists. If you find anything it would be wonderful. Keep in touch. Pam