Roxborough is still alive, somehow, and still in the tank. Alice was simply keeping him from ever being able to get out of that tank, because she wanted him to suffer. Of course, she ran into Jormungand during Crash 2.0, so she's likely not around any more, so who knows what will happen in the future?
As for who emerged first, that is unclear. Likely Mirage and Alice both emerged around the same time, while fighting the Crash Virus. However, both stayed relatively low profile for years. Alice blended in as a hacker in the Matrix, and Mirage simply orchestrated things behind the scenes. Morgan/Megaera emerged in the 2050s, and began following Dodger around. They were a really cute couple, too. Still, AIs were mostly the stuff of legend, even though a few people in the shadows had first-hand knowledge of their existence. It wasn't until Deus stepped out in the open by taking over the SCIRE that they became an actual fact, and not a myth. A good analogy would be dragons, before the Awakening, and then suddenly Ryumyo shows up over Mt. Fuji.