Well, as I'm sure as with your own children,
The fear escalated from the spider, that is where it began. Now it's shadows, boxes
I know your pain...neither of my kids are good at being alone. It drives me NUTS!
For the spider problem, if it is a real fear,I would talk about how you keep him safe. Maybe even try some gimmicks like "Spider Spray" or a bug catcher. Any chance he likes Spiderman? Maybe you could tell him it is spiderman checking in on him?
Finding the balance is always so hard. Before we get to a fit, I try and back away and decide is it behavior (in his control) or Sensory (and on this board we all know it is sometimes hard to tell!). Then, I treat it depending on the moment.
Good luck...let us know how it is going.