Ah, let's see...this is kind of hard. I'm a little too used to writing in my CT world which is purely mideaval and fantasy, so I'm trying to get myself a little out of that headspace and remember that Guardia ca. 1000 has teleporters and clocks and such. I've only read the first chapter so far, so I kind of relied on the synopsis for the second.
So...where is this? Feona's forest? That seems a little ways away from the Zenan bridge, I should think. By my reckoning, in a realistic sense, wouldn't that be at least 2 days walk? Nevermind. Let's see... well, I believe that making it the enforcers from the future may work pretty well. It would confirm his fears, and set up somewhat of a chase that I think you said will continue throughout much of the story (right? You did say the enforcers are trying to hunt him down, right?). Perhaps this time he easily slips away from them, but knows that he will need to be cautious in the future. Such a thing would set up the element of constant peril that he is in. Personally I would make it someone from Guardia; I'd make it a knight errant type out in search of quests (in the old Aurthurian tradition of questing knights), but that's just my own style, I think. No other fanfic I have ever seen lends itself to such mideval styles.
The split in Magus. Ah, interesting thing. I do something vaguely like that in one segment of my story (though in this case it is a spell of Magus' done to Schala). I make it corporeal being, explaining it as being an Egyptian trick (the Egyptians had a very interesting idea of there being a "double" to a person's body.) A reference to the ancient mythology I love so much. Anyway, in this case it is the time machine that does it. The time machine has transported not only his spirit, but his body as well. Therefore I see no reason that only his spirit should be split. I rather think that it should be a second of him, though be careful how you use such a thing; it could get very difficult to have two Magus', and it may get tiring to have to explain to every new person that there are now two of them. Hmmm...maybe he becomes a decoy to the enforcers for the real Magus, at one point? Just an idea.
Let's see...Time Egg malfunctioning? Good idea. Remember, though, that the Time Egg is never portrayed as a device as such. It is more of a mystical artifact that has always changed things for the better. I think, therefore, you should make it that, while Magus doesn't go to where he intends, it is where he is meant to go. You could make that apparent later.
Just remember this: there are thousands of fanfics out there. There are five hundred on FF.net alone. This means that a LOT of things have been done before...not just once, but a dozen times. The trick is to do something new that has never been done before. I myself have done so in giving it a very fantasy/midieaval feel (attempting as much as I could to add some elements of the style of LOTR), and removing near all that was scientific. Even Lavos is changed; I consider him a Dark Lord, a tyrant come from the stars to expand his kingdom. I have rarely seen either done, and neither, especially not the last, done to the extent that I do. This is my own stab at originallity in a very written-out field. I think at times I may vary so far that it might lose sight of the source...but I guess that is the trade-off. Anyway, just an admonishment. Keep writing.
