I do think it would be better if he just had one crate. Is there a reason he can't stay in the same crate he sleeps in at night now during the days?

Chewing up bedding is a fairly common problem. Every now and then one of my dogs gets a wild hair and shreds his bed. I have a carpet remnant in there with him now so at least he's not on the hard plastic.

This may be something that you might just have to experiment with and wait out. Three weeks is not very long to be with you and you're still getting to know each other. What works for one dog to help with this problem would not work for another, so there is an element of creative problem-solving.  With one of my dogs he howled and barked all day in his crate, but I gave him his own room, totally dog proofed and with a nice comfy old recliner in it to sleep on, and that solved his problem immediately. The other has to be crated because of serious separation anxiety but I had to find the right kind of crate for him (the metal ones freak him out completely--too open and exposed--he needs a plastic crate).

The not eating until you get back sounds like some mild separation anxiety (just the barking alone isn't really indicative of SA--lots of dogs bark when alone and lots of actual SA dogs don't make a peep), and you may want to talk to your veterinarian about a medication like Clomicalm to help him with his anxiety until he gets more settled in to your house and you get things to an optimum level of comfort for him. There's also a product called DAP (Dog Appeasing Pheromone) that you can buy as a spray to spray on his bedding or the area near his crate, or as a diffuser that you plug into the wall. You can get that at most large pet stores. But with all of these things, there's a variable level of efficacy depending on the individual dog. It is definitely no fun going through the experimentation phase, but once you find that magical combination of things, it is such a relief and it just becomes part of your routine.

Get your dog into a routine is important.  I just posted a blog on a cool new product that I bought, that entertains your dog while you're at work.  At the very least he could be entertained and not go so crazy.

Also, I had set-up my downstairs crate in the kitchen and gated off the kitchen.  This would allow him a bit more freedom.  But remember, not to leave any climbing aides like chairs.  This one day, I lost two apple pies when he maneuvered the chairs across the room to climb up to the counter.  

Good luck, keep in touch.