The name of the mother, or mothers, of William's two oldest sons, William and Robert is unknown. William appears to be the father of these two men and probably was, with a high degree of certainty. They probably both have the same mother but there is no primary record evidence which tells us whether that is true or not.
James Daniel, son of Jochebed,? a later wife of William Daniel was likely a child by a husband previous to her marriage to William Daniel. It seems likely that Jochebed was visibly pregnant when she was married to William Daniel as his will strongly suggests that James was not treated equally to William's other children, though William considered him to be his son. The surname of Jochebed's previous husband is not proved, but descendants of James have strong Y DNA matches to men with the surname of Davis. There were Davis men active in the vicinity at the time of William's marriage to Jochebed but those Davis lines later left Middlesex and primary record evidence does not link Jochebed to any Davis man or to a previous marriage.
William and Jochebed Daniel had a son named Richard, who had male descendants, but none have yet been proved in primary records. Y DNA testing of a proved male descendant of Richard Daniel should resolve this issue. Hopefully.
Pam Miller is the expert on this line and has a web site devoted to the genealogy of the line of William Daniel. I looked at this line very closely for a couple of decades and my Daniels had close interactions to the descendants of James Daniel, son of Jochebed. Finally, many years later, Y DNA proved our lines were not connected and that James was not the son of William Daniel.
Pam Millier's work is deeply rooted in primary record and Y DNA research and I consider her to be the expert on this line. There is still a lot of incorrect information being propagated about William Daniel on sites like FindaGrave.com, etc., and in various print sources.
http://pamiller.net/genealogy/docs/danielmiddlesex/danieldna/index.htm
Best,
Kevin
Kevin Daniel