Hello Lois, You share my mother's maiden name, so I'll give what help I can!
A reliable source for Jonathan SHELLY and his family is the 1860 census. The original census sheet spells his name "Jonthan" so the free website, HeritageQuest.com indexes it that way.He's on page 541 of the Quakertown, Milford Twp., Bucks Co. census on line 19. The National Archives microfilm series is 658, roll 1083. You can see the images free at home at HeritageQuest through your library membership or Ancestry.com library edition which would be available for use at a library.
The children listed are: Barbara, Henry, Isakiah, William, Andrew, Mary & Sarah.John is NOT listed.If he was the eldest, he may have been on his own by 1860.And in fact there is an 18 year-old John SHELLY on page 260, line 29 in Quakertown. He was living with Levi BEAN, a blacksmith, and was himself listed as an apprentice blacksmith.
For information on deaths you might look for cemetery or church records.For those children who lived later into the 19th century, there may be obituaries.
Contact me directly if you have other questions on further research.