1.Keypad 1 is in the first research room. 2. There are 3 blueprints in total, so they each correspond to one of the doors in the "research" area. 3. Aim where the blueprint for the guard-bot says "danger" in order to inflict damage (Think House of the Dead)
Jed: Deadeye's isn't the secret ending; you have to play through on hard mode to unlock Neferiti's. Note: talk to her every chance you get in order to unlock it.
@Pokemon789: The achievement you're talking about is called "Time Paradox", and for good reason. There are others for in-game events (like buying the last weapon) but that one is probably the most mod-based of all.