Part I

1. If you've read the documentation, it should be obvious.
2. Various library files should be helpful also.
3. If you still haven't figured it out, the message from Dr. Perelman about half an hour into the story should be a dead giveaway.
4. You must enter Simulation Mode and make the recordings that Dr. Perelman asks for, in order to test the validity of the Plan. This is why you were "awoken" ahead of schedule.