This is AMAZING! I've always wanted an alternative start mod that allowed you to start the game before the Emperor's death! My only gripe deals with the way you'll handle the death of the Emperor. For example, it's known that he died on the 27th of Last Seed, year of Akatosh 433... Perhaps you should allow the player to choose on what day he arrives to Cyrodiil and then if the player goes to jail somewhere between 21st through 27th of Last Seed, the regular tutorial will begin. Otherwise, the Emperor will just die and you'll need to stumble upon the Amulet of Kings somehow.
Really though, this mod would have a likely place in my load order if you could just keep the lore intact (Emperor dying when he's supposed to) and give options for characters who don't want to start in jail. Nonetheless, this sounds like my dream mod come true.
By the way, how will this mod affect Kvatch revival mods? Perhaps you could make this mod one of those as well, though it does seem a tad bit unrealistic to have a city built exactly the same way it was before its destruction.
I'm anticipating this soooooooo much. So very, very much.
Now, to GangstaWolf's original post.
I believe that it could be worked that, as in the regular main quest, where you and Baurus stay with the emperor in the dead end, the events still unfold without you. As is usual, you having almost no sway in the battle, the other blades die, and they had originally handled all combat for you too. When that assassin popped out of the wall, I NEVER managed to kill him. Baurus always did. So, Baurus takes the amulet to Jauffre. Jauffre, in turn, puts out a bulletin for worthy adventurers or mercenaries to aide him in escorting someone from county Kvatch to the Priory. As you eventually arrive at the Priory, a terrified monk walks up to you, pvssyring about a terrible siege, and hands you a copy of the Black Horse Courier before walking away. You read it (Journal update for those lazy buggers), and head upstairs to Jauffre. Jauffre recognizes you from descriptions given by Uriel Septim, as they were in close correspondence. The Main Quest takes off from there as per usual.
Now, a question.
I have a mod, you may know of it, called Enhanced Daedric Invasion. While I don't use it to full settings, it DOES come into play immediately after you close the Kvatch gate. Would your mod effect this at all?
EDIT: Also, willing to beta test if you want. I've got a sturdy comp.