these are al the ones you need:
train:
1. Player's Manual 1 (Rebecca's Start Items)
2. Player's Manual 2 (Restaurant Car - Train 2F)
Automatically given to you after Billy saves you)
3. Court Order for Transportation (Rebecca's Start Items)
4. Hookshot Operator's Manual (Rear Carriage - Train 1F)
Automatically given to you after you acquire the Hookshot
5. Investigation Orders (Cabin 201 -
Train 1F On the lower bunk bed)
6. Notice to Supervisors (Dining Car - Train 1F
On the small table at the foot of the stairs)
7. Passenger's Diary (Cabin 202 - Train 1F
On a suitcase underneath the table)
8.Brake Operation Manual (Engine Cab - Train 1F
Automatically given to you when you first enter this carriage
9. Note from Conductor: Conductor's Office - Train 1F
On the floor next to the desk
training facility:
10. Regulations for Trainees: Lecture Room - Training Facility 2F
On one of the multiple desks in the centre of the room
11. Notice to All Staff: Living Room - Training Facility 2F
On the table next to the armchair
12. Marcus' Diary 1: Marcus' Office - Training Facility 2F
Underneath the chess board on the desk. Solve the puzzle to reveal it
13. Assistant Director's Diary: Assistant Director's Office - Training Facility 2F
On the desk opposite the fireplace
14. About the Power Regulator: Torture Room B - Facility Basement B1
On the floor next to the door
15. A Verse of Poetry: Private Study Room - Training Facility 2F
On the edge of the central table
16. Management Trainee's Diary: Bunk Room B - Facility Basement B2
On the table in the middle of the room
17. Microfilm Image: Projection Room - Training Facility 1F
Acquired by inserting the Microfilm A and Microfilm B into the projector
18. Inmates List: Basement Save Room - Facility Basement B1
On the table next to the entrance
19. 1st Investigation Unit Notes: Medicine Room - Training Facility 2F
On one of the bunk beds
laboratory:
20. Marcus' Diary 2: Library - Laboratory B2
On a table at the end of one of the bookcases
21. Old Photograph: Marcus's Study - Laboratory B2
On the bookcase
22. Investigator's Report: Operating Room - Laboratory B1
On the floor next to the operating table
23. Leech Growth Records: Leech Laboratory - Laboratory B1
On the table next to the microscope
24. Laboratory Manager's Diary: Leech Room - Laboratory B1
On the chair next to the computer desk
25. B.O.W. Report: Breeding Room - Laboratory B1
On the floor amongst the breeding cages
treatment plant:
26. About Battery Fluid: Lodgings - Treatment Plant B6
On the south east bunk bed
27. Investigator's Report 2:Generator Room 2F - Treatment Plant B5
On the dead body in the south west corner
28. Treatment Plant Manager's Diary: cargo Control Room - Treatment Plant B7
On the floor in the south west corner
29. Gate Operational Manual:Cargo Room - Treatment Plant 1F
Automatically given to you when you plan on opening the shutters
these are all the files there are