What vital records show Mary Holmes as James's mother? The only info I've seen suggests that Mary and James (b. 1674?) were about the same age. Her mother Jane/Joan Freethy seems to have been born after 1640, m. "by 1671" to Thomas Holmes; one of their sons (Thomas Jr.) was born about 1670 and another (John) was still living in 1758. Doesn't it seem more likely that Mary married Walter in the early 1690's and was baptised with him in 1725 as stated in the Genealogical Dictionary of Maine and NH? I would be happy to see any contradictory evidence.
My descent is from James and Dorothy's son Elijah, who was the grandfather of Samuel Allen of York ME and Washington/Morgan/Noble County OH.