You've probably already worked this out but, just to clarify, CITS LPTE is what it reads after it's been coded, so to get the original words you have to do the coding in reverse. I should have made that clear from the outset.
An ingenious and well put together puzzle, but I just wanted to check whether I'm missing something. I discovered the method about halfway through so I don't get what the "fantastic endgame" is in message 13.
Orson, I felt much the same about the 'fantastic endgame'! I enjoyed the puzzle, but cracking the code was the major, pivotal part - I wouldn't call that the 'endgame'.