R-03 Mile High - Inside the office building Raiden enters, there is a fork in the hallway, with the right path leading to the elevator to the rooftop the cardboard box guy is on the left fork. Check that room for the cardboard box guy. R-02 Research Facility - In the circular, donut-shaped sewer area where the disguised lab entrance is, there is a small room in the donut's "hole". The cardboard box guy is hiding in one of the shipping containers.
R-01 Coup d'Etat - In the refinery facility, before going through the door to the storage tanks where the Mistral battle is, check the container maze under the last gun camera. You can find five cardboard box guys located in several of the Story mode's chapters, as indicated below. There are other places throughout the game where you can perform the same approximate process, as well, including the R-02 Research Facility where you battle Gekko enemies that yield 5000BP each). You can open the chest again for another 500BP. Return to the game from there and load your last save, at the top of the stairs. Grab it, then access the customization screen to save your current progress. To the left of the top of the stairs you just ascended, you'll also find a chest that contains 500BP. At the top of that area, you'll find a checkpoint. Near the second level's midway point, you'll ascend along apartment building rubble.