Two fresh points:-

THe undated circa 1490 Liber Assed discovered by Michael Crellin in the 1960's discloses that the Christians did not hold Milntown at that date - it was held by William Thwaites.

Far from eliminating the 'Mac's, I am beginning to get the feeling that they were being added by some of the early administrators. What do we make of McStoile (said to be an English name Stowell) and Mac Cletter (said to be Eng. P.N. Cleator)
Also has anyone studied Bod[d]agh which became Boyde. Could this be a name of status, held by servants on the Bishop's landed estate?