I would definitely move the crate into your room for the time being. If he is whining and doesn't have to go pee, just stick a finger in his crate for a few seconds to let him sniff and lick and he will know you are close by.
Also, we've found with our new, young foster dogs that sometimes they are just missing their siblings that they are used to sleeping with. We toss a big stuffed animal dog in the crate with them and they usually cuddle up to it and settle down. And also, if the dog is whining or throwing a fit, never let them out of the crate until they calm down and behave in a positive manner. Good luck!