This is not my line, but I think it would be quite kind if the document is not too long to transcribe it into a message here because a lot of folks do come from that lineage.
I am looking in my copy of Golda Rideout Soffe's book and what I notice is that all the children you mention (in the will) are those of Benjamin's second wife, Sarah Taylor. Your John is of Benjamin's first wife, Dorothy Thompson, according to this book. Since Benjamin died in 1819 (again according to this book), when John was already 52 (b 1767), it seems to me that your dilemma has at least two possible solutions, both of which I have seen in other branches of my family.
1. Benjamin may have already given to his "first family" whatever he wanted them to inherit, while he was alive, perhaps to avoid fighting later; 2. His first family may not have inherited anything from him.
There is always the possibility that this first family was not really his, I suppose, but that seems less likely as it is pretty well laid-out here.