This table is taken from `Kilrush Poor Law Union and the Parishes of West Clare' in the Clare Association Yearbook 2014 pp.46-50:

Notes to Table:

1. Generally, birth and marriage registers have survived, but there are some gaps, and very few burial registers were kept. With the exception of the earliest register for Kilkee, these registers have been microfilmed up to around 1880 and are available at the Local Studies Centre in Clare County Library in Ennis and at the National Library of Ireland in Dublin and can also be ordered through the Family History Centers of the Church of Jesus Christ of Latter Day Saints in Ireland and worldwide.
2. The townlands of Bellia, Cloonconeen, Killeenagh, Killinny and Knocknagarhoon, along with parts of Trusklieve and Tullig, are in Moyarta civil parish but in Cross Catholic parish (Paul Murphy, Cuchulain’s Leap (Loop Head): A History Of The Parishes Of Carrigaholt & Cross (1st ed., Carrigaholt & Cross Heritage Group, 1992), p. 243.)
3. The townlands of Lisgurreen and Lismuse, and possibly part of the townland of Carrowblough More, are in Killard civil parish but in Kilkee Catholic parish; and part of the townland of Farrihy in Kilfearagh civil parish may be in Doonbeg Catholic parish. The present area of Kilkee Catholic parish is over 10,000 acres, including land gained in a territorial adjustment with Killard in 1854, leaving 16,323 acres in Doonbeg Catholic parish. In 1851, the civil parish of Kilfearagh comprised 9,870 acres, 2 roods and 38 perches and that of Killard comprised 17,022 acres, 1 rood and 1 perch (Joe Hurley (ed), Doonbeg: A Story to Tell (Doonbeg Book Committee, 1995), pp 12-13; and Ignatius Murphy, Before the Famine Struck: Life in West Clare 1834-1845, (Irish Academic Press, 1996), p. 11.)
4. The townlands of Carrowduff, Doonsallagh East, Doonsallagh West, Killernan, Knockanalban, Knockloskeraun, Shanavogh East and Shanavogh West in Kilmurry (Ibrickan) civil parish (no. 40 on the map) appear to have become part of Miltown Malbay Catholic parish (no. 39 on the map) in 1839 and part of Ennistimon PLU in 1850. This move straightened the meandering boundary between the two civil parishes and between the original 1838 PLUs which can be seen on the map.
   Further comments from Donal de Barra:

   The early history of the boundaries between these two parishes is obscure and is complicated by the one-time existence (as I believe) of a parish centered on an Augustinian monastery near the present Killernan Graveyard. The territory of that parish may have extended to Cahermurphy in Kilmihil.

   It is certain, however that two separate parishes – Kilfarboy and Kilmurry Ibrickane have existed, at least since the McGorman migration in the late 12th century. The RC Church merged the parishes (like many others) in consequence of the Penal Laws (although Fr Ryan, History of Kilmurry Ibrickane says that they were held by a single Priest prior to the Reformation), and, as you say, they were separated again in 1839.

   As part of this separation the clergy (presumably Fr McGuane?) chose to ‘regularise’ the boundaries and based a new boundary on the river Annagh (as you say). This meant that Carrowduff, Doonsallagh East and West and Knockliscrane all moved from Kilmurry Ibrickane to Kilfarboy. I am not aware that Knockanalban or Shanaway East or West ever changed parochial sides!

   In this area it is the norm for Townland boundaries to follow watercourses, where possible, but there is an exception in the case of Killernan which straddles the Annagh river. The clergy opted to stick with the river as their new boundary and so Killernan was split in two - part in Kilfarboy and part in Kilmurry Ibrickane. (This also applies to Doonsallagh West, but the small isolated portion has no dwellings).

   On the North side of Miltown Malbay Parish, Rineen School is under the care of Fr. Murphy (Miltown) even though the townland is in Ennistymon civil & R.C. Parish.

   The Miltown Parish website has a Millenium Census conducted by Fr. Seanie Murphy, who visited all the houses of his parish for his census and so delineates the R.C. Parish, with Moy being a subdivision thereof. [The townland names and numbers are not lined up in rows in the online version of the Millennium Census!]

5. There are probably other similar discrepancies between the other Catholic and civil parishes in the above table known only to those with local expertise. I would be happy to hear of any such discrepancies.