I think you have this Thomas mixed up with his grandson.

Question

The boys you have listed as his brothers were this Thomas's grandchildren.  John was his son.  John had 3 sons.  One he named Thomas.  Here is where the confusion comes in.

Comments

I removed him as the son of his son and left him as a father only instead.  Now it appears at least chronologically possible.  

Thanks for pointing that out!  :)

(There could still be the need to add another grandchild named Thomas)