I'm not an expert but I'd say the chinchilla is just freaked out by the whole experience, being moved around so much. It's food may not be ideal, but I wouldn't start changing it over for a few days until it calms down, just leave it alone in a quiet room and I guess a raisin wouldn't go amiss.
Cheech barks when she's too hot, so maybe check the temperature. Get it to a good vet for a check over and find out its sex so I can stop calling it an it. But it might be best to make sure it's not ingested too much plastic, check the poos and how much it's eating.
It's always traumatising for any animal and the best thing might just be some peace and quiet and some proper care. I'd say the noises are just warnings because it's scared. That's my opinion anyway. Hope it's useful.