I have been meaning to say something on here for a while now.
First of all, two huge thumbs up for Prophet's Guile. The only problem I had with it is the same problem I have with the original Chrono Trigger - Too easy, dungeons are too short. Which isn't actually a "problem" at all, I guess. I find most RPGs to be too easy, but that's just me.
As for the discussion of how Magus speaks as the prophet:
Yes, I do agree that it seems a bit overdone and strange, but I think it fits in very well. He's not trying to be Magus, since Magus is Janus and everyone would be able to tell. He's trying to seduce them into thinking he's a wise prophet, even wiser than the 3 gurus, so therefore, I think the weird overdone manner he speaks in suits the situation perfectly.
Furthermore, the text at the beginning and end from Radical Dreamers is cool too, nice touch. And the artwork is VERY nice, I'm shocked you were able to make it look that good with the limit on colors and what not. Very, very good job. I'm a picky guy when it comes to hacking stuff, also. This feels like it was meant to be there, like it came from the guys at SE themselves. Well done, I consider it an official part of the CT storyline now. ^^
Hopefully this thread hasn't been too long gone and you get to read my statements here, because I've been meaning to praise you for a while. =\
Anyways, nicely done.