There is a ribbon cable in the backbox that connects the MPU board and the Driver board. It's the short, horseshoe looking, wide cable. Unplug both sides of that ribbon cable and reconnect it. Make sure to align the pins correctly because it's really easy to accidentally move up or down one pin. The behavior you are describing sounds like the MPU and the drivers aren't communicating well.
The bookcase has two limit switches and on startup, it will go back and forth between them to make sure they both work. If either of them isn't communicating with the MPU then it will just keep running.
What is with the alligator clips?