The notes can all be found when you are able to switch between characters. You must be playing as Delta-Six to find the notes

Note 1

This note is located in the elevator on the left
Edit: I have been told that the note can appear in either of the elevators

Note 2

This note is located by the door oposite the gym

Note 3

This note is located on the far right of the blue test area

Note 4

When you meet Epsilon-Five after finishing the tests this note will show up at the location of note 1 or note 2

The Magazines can all be found when you are able to switch between characters. You must be playing as Azriel to find the Magazines

Magazine 1

This can be found in the area with the three dead bodies, it is located near the ladder


Magazine 2

This can be found in the area with the boarded up doorway, it is located under the dumpster


Magazine 3

To find this one you must use your foot on the muck infront of the Boryokudan HQ until Azriel mentions something coming out, it's located to the left of the muck

Each character shows up at a different point in the game, to find them you must be playing as Azriel

Spike

At the start of the game, after the Boryokudan break into Matthius apartment, instead of going in, walk back to the first screen.

Jet

When you are in control of both characters, walk back to Hibiscus Highrise and he is standing near the top of the stairs.

Ed and Ein

When you gain access the the Building Paul Erickson lives, go to the top floor and they are staning on the far right.

Faye

After curing Paul, go back to the area you found the Carbon Ray Stabilizer and she will be standing there.