Don't forget Alice started seeing something back when Connor was still interrogating Mark. Also: there's no evidence that Connor had yet released the group from the trance until he was finished talking to them, because he knew he was going to pass out and he had to keep their attention.
Who's to say Connor even had enough time to complete the upgrades? It might fall to someone else (Miki!) to do that.
I do think KK will whip something together in record time, but it will be a countermeasure. Whoever is in that Sikorsky will get the first strike!