The murders in New Babbage appears to have been solved. Jason Moriarty confessed to killing the Professor, and with the murders being so similar it is assumed that he committed the rest as well. In the shopping alley, I discovered a book he wrote which provided an insight into his highly disturbed mind. The Professor's experiments has obviously unhinged him, and he felt betrayed when the Professor left him to his own devices and returned to working on the Porta Terrarum device, which appears to have been what caused his mental instability- he heard voices which may have originated from beyond our world, from one of the worlds touched by the device. The Professor was working on the device for the Thirteen, who were also seeking to destroy Moriarty. Perhaps the disturbance in his mind explains the clues left haphazardly, as well as his desire to seek attention and vindication for his actions, as he saw himself as so betrayed. It still seems a touch facile, perhaps, but then life often is. The Van Greed Society, the Thirteen, and the Masonic contact within New Babbage remain mysteries for another day.
The device located in the Bow Street Police office was a fake, as I suspected- it didn't make much sense otherwise (in fact, it made little sense for the police to display it so openly if even they believed it genuine). The real device was hidden beneath the theatre, and Moriarty used it to open a doorway to allow entrance to our world to monstrous things, which hovered above the theatre after the device reached some sort of critical mass. Professor Nishi underwent a transformation into some sort of creature herself, and fought them off. After the battle, she dropped to earth, apparently injured in some manner beyond the flesh, and disappeared before our eyes.
While it appeared that she might perhaps be gone from our world forever, it was revealed that in fact she was safe and sound, although drained from the experience.