Miguel is probably going crazy right now đ¤Ł. I'd look at Batman Supersoldier vs Spider-Man 2099 (Bruce will definitely go up against Miguel if he finds out about the Spider Society's Methods)
The Injustice Universe still exists, as per the laws of the Multiverse. Peter's interface simply created a branched out Universe that's shifted from it's original course.
Maybe you should do a status page. since even i forgot all of his power, in the early days i think he have a system which become useless now because he becomes independent