After some further research on the family of Conwy of Bodrhyddan, I made an interesting - and somewhat surprising – discovery. It appears that the descent of Capt. Jenkin Conway of Killorglin from the Conwys of Bodrhyddan, as shown in “Black Jack’s Book” on Mark Humphrys’ website, can be largely (although not entirely) corroborated by another source: Peter Bartrum’s Welsh Genealogies.
Mark notes on his website that the pedigree in “Black Jack’s Book” can be found in an 1872 book by Mary Agnes Hickman, Selections from Old Kerry Records. That book is available online her, with the Conway pedigree starting at page 50.
https://archive.org/details/selectionsfromol00hick/page/50/mode/1up
The pedigree from the book is as follows (slightly different than what is shown on Mark’s website):
1. Sir Hugh Conway
2. Richard Conway; m. Alice, daughter of Sir Henry Torbock
3. Sir Henry Conway; m. Alice, daughter of Sir Henry Croniker
4. John Conway; m. Jane, daughter of Sir Richard Ratcliffe
5. Jenkin Conway; m. [illegible] daughter of Meredith
6. John Conway; m. Jane Stanley
7. Pierce Conway; m. Jane, daughter of Jenkin son of Llywelyn
8. Henry Conway; m. Grace Dry [sic]
9. Jenkin Conway [of Killorglin]; m. Mary Herbert
The family of Conwy of Bodrhyddan is covered by Bartrum’s Welsh Genealogies in a series of tables named Conwy 1 through Conwy 9. The tables can be found on the Genealogics database here (scroll down to see the later tables):
https://www.genealogics.org/showmedia.php?mediaID=17217
The pedigree from Bartrum is as follows (the name of the pertinent table is cited at the end of each line):
1. John ap Richard Conwy; m. Marsli ferch Maredudd [Conwy 1]
2. Jenkin Conwy; m. Elen ferch Sir Henry Torbox [Conwy 1]
3. John “Aer” Conwy; m. (2) Janet ferch Edmund Stanley [Conwy 1]
4. Piers Conwy; m. Jonet ferch Jenkin [Conwy 4]
5. Harry “Yr Aer” Conwy; m. Grace, daughter of Hugh Drihurst [sic] of Denbigh [Conwy 5]
The pedigree then ends with a list of the numerous children of the last couple - including a son Jenkin, who has the notation “Captain”. This is presumably Capt. Jenkin Conway of Killorglin.
Obviously there are some notable differences between the two pedigrees, but they clearly are covering the same descent. FWIW, my guess is that the Bartrum pedigree is the more accurate one, since it's likely based on pedigree manuscripts that Bartrum had reviewed.
Bartrum's pedigrees generally end in the in mid-1500s. Because of that, I haven't been able to determine how exactly Jenkin Conway's wife Mary Herbert fits into the Colebrook family.