I don't believe there could be a father-son relationship. John Trotter first of Mortonhall had a younger son James who was born/baptised in 1612. He wouldn't have had two sons named James. Further, if Trotter-784 was his son then he would have been the eldest and would have inherited the estate and not gone to America. That tended to be done by younger sons.
There are several John Trotters, especially over in Fife.