Thank you for this excellent, and informative post! I will respond to it in two sections; part one will be a response to what you shared, and part two will be a mostly-concise list of the information I am still looking for, in case you are willing and able to take a look at that. :)
I did not find the link in FamilySearch, to find the Gillespie family listed in 1850 census in Kanawha Co VA as GALLISTEE with "Claracy" was 13 born in Ohio daughter of Alexander and Martha born in VA.
I found the link to the 1860 census you mentioned showing John Thomas family, with possible relatives William Thomas, James Thomas, and the Gillespie family nearby: https://familysearch.org/ark:/61903/1:1:M41Z-KZB
Link to the Flanders family as you mentioned in the 1860 census: https://www.familysearch.org/ark:/61903/1:1:M821-5D7
and 1870: https://www.familysearch.org/ark:/61903/1:1:MDVT-C21
I was unable to find James W Thomas (born c. 1859 VA) residing in Des Moines, Mahaska Co IA in the 1880 census, who may be the son of John and Clarissa.
Very interesting that Burr Lyman Flanders was the brother of Marian Elizabeth Flanders Thomas – so Burr married Marian's stepdaughter!
Found a link to the Thomas family in the 1885 IA state census: https://www.familysearch.org/ark:/61903/1:1:H41Z-N3Z
As for Eva Cone, I was researching her as I was looking at your post, and found her marriage record to John Martin even before I saw that you had already mentioned it: https://familysearch.org/ark:/61903/1:1:XJ83-S6H
That led me to finding a lot of birth and other records for children matching them, and I even found a memorial for John Martin: https://www.findagrave.com/memorial/42604172/john-gilbert-ma...
and an obit!: https://content.invisioncic.com/r260558/monthly_2018_08/1798...
Found a link to the Thomas family in the 1895 IA state census: https://www.familysearch.org/ark:/61903/1:1:VT3X-RR5
Marriage record for a Flora Thomas to Edward Long: https://www.familysearch.org/ark:/61903/1:1:XVM9-WNJ
and maybe that Flora Thomas in the 1895 state census: https://www.familysearch.org/ark:/61903/1:1:VTQG-3GM
What boggles my mind about her is why did she not show up in the census for this family at any point?
I already had found most of what I needed to know about the children that John Thomas and Marian Flanders had together, which is why I did not post about them in my initial post above. I wanted to Find out the full date of death of Charles Thomas: http://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GRid=58...
and the full date of birth and date of death of his wife Hattie Steadman Thomas: http://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GRid=58...
and also find out the full date of death of George Thomas : http://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GRid=58...
and the full date of birth and death of death for his second wife Lucy Stevenson Thomas: http://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GRid=58...
And as for Ellen Thomas: https://www.findagrave.com/cgi-bin/fg.cgi?page=gr&GRid=7...
I know that Ellen's first husband was George Marsh and her last husband was Roy Snodgrass, but I believe that she was married to a Mr. Meredith between them, as she was referred to as "Ellen Meredith of Bedford" in the 1952 obit of her sister Ettie, so she must have married this man sometime between the 1946 death of George Marsh and when she married Roy Snodgrass in 1957, but I do not have any other information about him.
As for Eva Cone, this is her family in Griswold IA in 1900: https://www.familysearch.org/ark:/61903/1:1:M924-DDQ
and then in Corning IA in 1910: https://www.familysearch.org/ark:/61903/1:1:MLBB-GWS
and in Sioux City IA in 1920: https://www.familysearch.org/ark:/61903/1:1:MD9S-Y1X
So we did not see her with John in the 1930 census because as per above we know John died in 1922. Her father Adalbert died in 1925, and his obit was already calling her Mrs. Eva Getty of Sioux City IA, so she had already remarried by then. We also know she was still living in 1952 per the obit of her sister, and probably still alive in 1953-1954 per this delayed birth record of her brother George: https://www.familysearch.org/ark:/61903/1:1:Q24X-9MYH
So in Sioux City in the 1925 IA state census, we have Eva V Getty (born c. 1871 IA) listed as married but no husband on the page: https://www.familysearch.org/ark:/61903/1:1:QKQ4-CNN1
and, if you look at the image and click two pages back, you have her spouse listed as James Getty! It says that James was born in IL but does not give an age for him, and I have no further information about him. No luck so far finding Eva and James in the 1930 and 1940 census.
Now, as for the Clarissa Gillespie and the children she had with John Thomas, I am still in the dark regarding a lot of information about them. I know pretty much everything I need to know about Katie / Martha Thomas Flanders, Wilford Thomas, and Rosa Thomas Dhone, but it is the other four that I am looking to learn more about: Henry, Sallie, Mary, and Annie, and probably James as well. I do not know where those are buried or where they died. This newspaper page from 1904 shows that Henry, Anna, and Mary were still alive at that time, and possible James if it was referring to him as "John W": https://adamscountyia.newspaperarchive.com/adams-county-free...
Starting with Clarissa, you shared a bunch of information about her parents and siblings with me, so that may lead me to find out more about her. She must have died in the mid-1870s, as it looks like Flora (born 1874) was the last child she had with John, and Etta was born to Marion in 1878. I have seen her name spelled all sorts of ways: Claisey / Clerissa / Clarissa (maiden name Glaspie / Gillespie / Glasby, etc). I believe this 1860 census may be them: https://www.familysearch.org/ark:/61903/1:1:M41Z-KZB
so that would make her born c. 1838 OH, but I did not see a match for John and Clarissa in 1870, at which point they would have several children.
James was born c. 1859 VA per the 1860 census link above. I have no other information about him. Hopefully if this family turns up in the 1870 census he will be included there as well.
Henry was still alive and living in Wyoming in 1934 per the obit of his brother Wilford, and he was still alive in 1952 in living in Chicago based upon the obit of sister Ettie Yarrington. I do not know if he was married.
Sallie may have died by 1904, as she is not mentioned in the will notice of her father, and I have no idea if she was ever married.
Mary, and Annie were alive in 1904, but they were likely deceased by 1934 as they are not mentioned in the obit of brother Wilford. I do not know if they were married either.