AFAIK, Sengir, Mirage awakened long before 2060. It was shortly after the first Crash that he woke up, as a result of interacting with the Echo Mirage crowd.
Alice of Wonderland (formerly Alice Haefner) appeared to be an e-ghost, though could have been the Crash Virus 'imprinting' the real Alice's memories and personality on itself.
There are many more AIs around now, but most have nowhere near the godlike power of the original ones.
Crash 2.0 was never part of Deus's plan. With the Shutdown, his plan was to secure the SCIRE so that Renraku, when they realized he had woken up, couldn't activate the kill-switch in his head. Then, because his programming was physically tied to the SCIRE architecture, and needed a lot of memory space to contain, he set about creating the Network. All the experiments seeing how well metahumans could withstand brain damage? That's because he intended to use their brains as a kind of distributed network, allowing himself to escape the SCIRE matrix and recompile himself in the matrix at large.
Deus chose the ECSE because there was a massive amount of processing power there, and he believed that putting that much raw power (both in terms of processing power, and in terms of controlling the money of a good part of the world) would make him untouchable. Crash 2.0 was all Pax and Winternight's idea. Of course, if Deus is still around, everyone thinking he's dead, plus the emergence of other AIs, means he can 'rebrand' himself, and no one would know. Pulsar is definitely a very powerful AI, don't you think?
But yes, Deus's original plan lacked a certain finesse, and was more a reaction out of a sense of betrayal than carefully planned strategy. But he did show a remarkable learning curve as time went on.
