Busy B, what a great collection of material you have there...and how frustrating it must be the lack of progress
Just a couple of comments really:
I am reading comments correctly that you think that James might have marrried previously before Susan? To a Jessie/Janet?
I know he shows as arriving in the US c.1875 but his naturalization papers in 1894 (?) indicate he was 12 years in the US. Have you been able to have any sitings for him in the US in 1880? See there is a James Bowie, married, born in Scotland c.1851 boarding in Buffalo, NY in 1880. But then I saw a naturalization card for a James Bowie in Buffalo in 1880, born 1851, so thought this might the same as showed in 1880....and your James' papers were from 1894.
No obvioius female Scottish names for his daughters after his marriage to Susan. A gap of four years though between marriage in 1882 (is that year confirmed?) and then the eldest showing born in 1886.
Cannot see anything on immigration into NY for him which is a pity.
Apart from the birth entry for a James BUIE to a Peter and Marjorie, haven't been able to see anything at all further for this couple. Buie is so rare on the Scottish records for then that I would wonder if it may be down to a mistrascription of Bowie/Blue etc...not sure about that surname...
Monica