Dear B, have we been in contact before?
I went firstly to the 1901 Census and found 16 Quills living in Tralee. I followed their marriages in hopes that one of them was another child of John Quill father of Margaret who married John Worthington. I found William, James, and Thadeus so far as fathers for Quill couples marrying between 1857 and 1881 in Tralee but no John except for his mention as the father of Margaret in her 1861 marriage.
This is a bit of a reach but I found a Margaret Quill as godmother to John Quill, son of John Quill and Margaret Commane in 1861 in Tralee
http://churchrecords.irishgenealogy.ie/churchrecords/details/7807070479839
What appears to be the same couple have another child Bridget in 1858
http://churchrecords.irishgenealogy.ie/churchrecords/details/021ad90478491
I was unable to find a record of the marriage of this couple at this time.
Griffith's Valuation gives 18 returns for John Quill circa 1853 in Kerry but the 4 listings for Ballymacelligott and Ratass are probably the most likely. Rathass is now part of modern day Tralee. The 2 enties for Ratass/Rathass are very interesting as they give CAPTAIN John Quill as the immediate lessor of Timothy McMahon and John Connor.
There are 3 Quills listed here in 1870 as landowners
http://www.igp-web.com/IGPArchives/ire/kerry/censubs/ker-landowners-m-q.txt
I have been unable to track down Captain John Quill as yet but must go now as the morning is gone. Do let me know if any of this is new to you or leads you closer to your family.
Warm wishes
Martine