Hi cdn
Sorry for taking so long to answer. I haven't looked into our tree in so long I wanted to refresh my memory before assigning what we know to a reply. I have added my answers into your post in brackets.
Charlie J,
What a delightful surprise to hear from you! I am eager to collaborate and will consider collaboration valuable even if it disproves what I thought I knew. My understanding of Irish records, place names, etc. is far from expert, so please don't be over-polite about disagreeing/correcting. That said, here is more about Jane and evidence by which I'm connecting my ancestor to yours.
(We also have a Jane Jones B1793 who married a George Browne 1811 and died 1874 who I have as a possible daughter to John Jones B1731. She had many links to Shepherd Jones B1814 son of John Jones B1781. Unfortunately a few years ago I lost most of my research, so not sure if I had concrete evidence how she is related. Fortunately most records were recovered plus many new records found. I think we can take it your Jane is the correct daughter of John Jones B1731 and I will have to try to resolve how my Jane is related and that's OK, it's all part of the journey.)
In addition to the son named John Shepherd (as spelled on his grave marker), she had another named William J. with strong indication the "J." stood for Jones. Indexed marriage records list Jane Jones and Thomas Condell, married in 1801. A newspaper marriage announcement from May 1801 says Miss Jones, the daughter of John Jones, Esq. of Hacketstown, married Thomas Condell from Carnew. I'm interpreting Hacketstown and Carnew as parish names here. A tithe applotment record for Eagle Hill, Hacketstown, Carlow dated November 1823 shows Jane Condell occupying land right next to that occupied by John Jones and Shepard Jones. July 1824, Jane and 10 of her children emigrated to the USA, where her branch has remained, as far as I'm aware. I haven't found records for Thomas or one additional daughter, but they did end up here, too, and it seems reasonable to believe that Thomas was already gone in November 1823. Deed memorial 490515, Book 717, page 379, having to do with Aunt Rachel Barker Marks bequeathing land to John Jones the younger, lists Thomas Condell as a witness.
(The name Shepherd(and all it's spelling variations) would most likely come from the previous owner of Woodside. A man called Anthony Shepherd. Aunt Rachel Barker Marks is believed to be a sister to Janes Jones nee Barker. There is another sister too but her name escapes me. Also I do believe Rachel and Thomas do appear in some documents as witness to a number of dealings.)
Looking forward to hearing your thoughts!
Have you figured out exactly how the older Shepard (the one on the 1823 tithe applotment) fits in? He seems like a brother to Jane and the younger John, but I have found nothing to confirm that.
(This Shephard Jones B1779 is a brother of John Jones B1781. His grave is shown in a photo earlier in this thread.)
There is another witness to the deed mentioned above whose name I can't make out. Possibly another brother-in-law? Do you know anything about that?
An 1838 newspaper death announcement says, "February 21, at her son's residence, Newtown, Baltinglass, in the 99th year of her age, Mrs. John Jones, relict of the late John Jones, Esq., of Woodside, Hacketstown." Do you have anything to corroborate or contradict that being our grandmother?
(This is Jane Jones nee Barker (Father Joseph Barker D1788) married to John Jones B1731. This makes her DOB circa 1740. Her Son was John Jones B1781 of Newtown Saunders and this is where I grew up. Also a photo of the grave can be seen earlier in this thread)
I have not, so far, found a concrete link to the Holdenstown/Rathvilly Jones before the mid to late 1800s but suspect there is one. It just needs the right document to be found. I hope this useful in some way. For me further research needs to be done in records offices which do not have material online. I just haven't had the time to do so.
Are you living in the US?