The Thompson family, taken in total, is quite a challenge. I have the William Thompson who married Jane (possibly Caldwell) as a POSSIBLE brother or other relative of Reverend John Thompson of Prince Edward County, VA (PECo; the Reverend came to VA via DE, then PA, and actually died in NC after leaving PECo). The Reverend John Thompson had a son named John Thompson, Senior who went to Campbell County, VA (he married Margaret Phair). There was also a Robert Thompson who was born in the 1690s who could have been yet another relative of this family.

William and Jane Thompson, whatever his relationship was to the Reverend (if any), had Alexander, John, Robert, Agnes (Thompson) Edmundson, Rebecca (Thompson) McNeely and Sarah (Thompson) Hendry/Henry. The above sons Alexander and John were deeded land in Augusta County, VA by their father William in 1751.

A John Thompson was also deeded land earlier in Augusta County, VA (area called Beverly Manor) in 1743. This land previously belonged to John Seawright. I do not know if this was the same John Thompson as above (i.e., the son of William and Jane Thompson), but I guess it could have been. This John Thompson died and left land to his son Thomas Thompson. Thomas Thompson ultimately deeded or willed this land to his brothers Robert Thompson (married an Agness) and James Thompson (married a Rebecca). Robert and James Thompson eventually sold the land to a Zachariah Johnston in 1773. Could this be your John Thompson?