I love this scenario and I'd love to see it done well, however, I think you made some strange choices in the beginning. I do not believe that the Mexica would have collapsed so quickly after Cortes is killed. Their empire didn't even collapse after Cortes took Tenochtitlan, it took a while for the Spanish to assert control over all of that territory. It's not that the Mexica were popular, they most certainly weren't. Lots of peoples wanted to see a new power structure. But they were very effective at keeping control of their territories. Really, the only way to destroy the Mexican Empire is to take Tenochtitlan.
Events in Tlaxcala also appear strange. No doubt a pro-Mexica leader would come into power after the Spanish are destroyed, but the way he does it doesn't seem realistic. The whole bit with the assassination attempt and everything...
There are several aspects of this TL that I do wish to go over again with a comb and redux my previous mistakes to the TL (Plus when I wrote this I had a balkanization fetish going on), but to answer your questions:
1-My view of the Mexica Empire is that it was not really a totally centralized empire, largely the Mexica keapt power through a combination of backroom politics and effective military forces. Many of their cities were keapt in line through political and military protection and garrisons of Mexica warriors. The breakup occurs as a result of panic from disease spreading its way through Mesoamerica, whereas dissenters or treasounous Mexica are making grabs for power. With pressure from disease, this internal revolt, and external revolts the Mexica slipped.
2-The Tlaxcallan Confederacy is much less centralized then the Mexica and the following events are apart of a powerplay, which results in Xicotencatl the Younger taking power and beginning to centralize through military action and discrediting the reputation of his rival.