The lists of words are verses from the King James Bible, with their words in reverse alphabetical order. The chapter and verse numbers indicate two letters which should be taken from the name of the book - that is to say, the full title of the book in the King James Version (for instance, "The First Book of Moses, called Genesis" instead of just "Genesis"), as hinted at by Morpheus's insistence on being called by his full name. The books should be arranged in reverse Bible order (that is, starting from Revelation and going back to Genesis) - in much the same way the words from the verses were alphabetized in reverse order.
NI The Revelation of Saint John the Divine 13:11 NE The Second Epistle of Paul the Apostle to the Corinthians 8:10 TE The First Epistle of Paul the Apostle to the Corinthians 13:3 EN The Gospel According to Saint John 3:29 TH The Gospel According to Saint Luke 1:2 CH The Gospel According to Saint Mark 12:2 AP The Gospel According to Saint Matthew 27:7 TE The Book of Daniel 1:14 RF The Book of the Prophet Ezekiel 14:9 IR The Book of the Prophet Jeremiah 25:22 ST The Book of the Prophet Isaiah 21:10 GO The Song of Solomon 7:8 SP Ecclesiastes; or, The Preacher 9:18 EL The Second Book of the Chronicles 18:26 EN The First Book of the Chronicles 26:22 DI The Second Book of the Kings, Commonly Called the Fourth Book of the Kings 9:20 NG The First Book of the Kings, Commonly Called the Third Book of the Kings 20:21 CL The First Book of Samuel, Otherwise Called the First Book of the Kings 30:20 AU The Fourth Book of Moses, Called Numbers 22:28 SE The First Book of Moses, Called Genesis 32:24
After the verses are arranged, reading the appropriate letters spells the message "NINETEENTH CHAPTER, FIRST GOSPEL, ENDING CLAUSE"; the last clause in Matthew 19 is the final answer: AND THE LAST SHALL BE FIRST.