Joseph Smith's scribe Martin Harris lost the only copy of the first 116-pages of the translation that would have been the Book of Lehi and the start of the book of Mosiah. In the Doctrine and Covenants, the Lord says that the manuscript was stolen by people seeking to undermine the work and commands Joseph not to re-translate this portion, but instead to substitute an abridged account by Nephi also contained in the plates.
Joseph Smith reported that most of the plates were sealed, preventing him from translating them. What was published as the Book of Mormon is only a fraction of what was written on the plates.
Author Allusion: The costumes that the townspeople wear during the "All American Prophet" number are recycled from Trey & Matt's first film, Cannibal! The Musical, which not-coincidentally was a musical with some Mormon jokes.
Development Gag: Cunningham's line in "All American Prophet" about how the Bible is a trilogy and the Book of Mormon is Return of the Jedi is a reference to an early version of the song about how the third parts of trilogies are always the best.
Elder McKinley is almost always referred to by the fan-created first name 'Connor'. Elders Church and Thomas are typically called 'James' and 'Chris', respectively. However, there's never been any official word on what the characters' first names are.
Trey and Matt originally wanted to make a musical of the actual Book of Mormon, feeling that the source material was already absurd enough. However, they backed off of this idea when they couldn't make a whole musical based around it. They instead opted for the musical segments in the South Park episode "All About The Mormons". These segments were described as "exactly as long as that joke was funny."
An early draft set the story in Somalia instead of Uganda.
"Turn It Off" was originally supposed to be sung by Elder Price in focus. This got changed when Parker and Stone decided that making Price an Armoured Closet Gay character was too much of a cliche.
The demo recording of the finale hints that Elder Cunningham was going to be killed and eaten by the Africans at the end.