Mike,
It appears that the father/son, and William of John and Martha Miller Montgomery descent are I1 and related.
It also appears that the sample from Nathan Montgomery/Illinois is not related to the above. I do not know why. This sampling indicates that the YDNA participant is not related.
This confusion happens all the time with Y-DNA. It is the best initial path to the truth. Because of the doubt this casts on the YDNA tests, more descendants of John Montgomery/Martha Miller need to be tested.
For all I know we are cousins because there is no YDNA participant from the Magoffin County, KY (my) neck of the woods that I know of.
I kind of wonder about the John Montgomery/Martha Miller connection to William Montgomery story since it was added to the Daniel Trabue book, Westward Into Kentucky as late as 1851, by his son James. Sort of as an aside to explain how the above was not related to another Montgomery marrying a Trabue.
Kay