I agree that the 3 generations of Samuels scenario is about the only way to explain all of the references over a period of many decades. As we put together more pieces of this mosaic the picture is beginning to emerge and make sense.
One of the key things that some of the later records clarify is a second specific location where the Samuel(2) Bonnell family lived. While they apparently lived in the Penn's Neck area near Princeton and near the western boundary of Windsor Township for many years it's now clear that they later relocated to Hightstown - which is near the eastern boundary of Windsor Township.
The questions regarding James English and Benjamin Ward are pertinent and help pinpoint the location of the Inn that Samuel Bonnell operated for several years. James English was the Inn Keeper prior to Samuel Bonnell and Benjamin Ward after Samuel. The brief references that I've found to them describe both as Inn Keepers at Hightstown. James English was later a miller and a blacksmith at Hightstown.
Hightstown was small and centered on the point where the Kings Highway crossed Rocky Brook - which is where Christopher Hoagland operated a mill from 1758 until his death in 1763. Since Hoagland owed William Bonnell a small amount of money at his death it appears very likely that William worked for him at the mill. So we can put a pin on the map at Hightstown, NJ as the earliest specific location where we have identified William Bonnell as living - at least from 1761 - 1763.
That location also helps explain some of the Bonnell records that involve people who lived in Monmouth County. Hightstown is just a few miles from Monmouth County.
It seems quite possible that Samuel Bonnell(3) served with the 3rd NJ Regiment (the New Jersey Greys). While the officers were mostly from northern NJ most of the foot soldiers were recruited from southern NJ.
John Bunnell adds:
That a Samuel Bonnell served in the Third New Jersey is beyond doubt. I have extensive references to pay, as well as the final pay settlement from 1785 signed by Jonathan Dalton (the youngest signer if the Declaration of Independence). The only question is whether this is for Samuel (3) or an unrelated individual. Interestingly, there is also a Revolutionary record for a Samuel Bonnell who skippered a schooner from Elizabethtown to deliver firewood to American forces.