The Wrench is found within the body of the dog-like creature strapped down in Bendy and the Ink Machine.
Where can you find the Wrench?
Exit the pedestal room and then follow the right turn. Across the hall there’s a character strapped in and presumably dead. I’m going to assume this is Boris, but I’m not quite sure at this point. I guess there can be more than one of each character floating around, but anyway, the Wrench is sticking out of its chest cavity.
Creepy.
Turn back down the hall. Set the Wrench on the middle pedestal on the right side.