Let there be...change

As you might have heard we recently adopted a dog, Cecil. He's a 2 year old border collie, hound, beagle mix. We know some of what he's been through just from what the rescue group told us after we adopted him and we're finding out much more as we go. We've discovered he's afraid of a lot of things even the cat. He'll whimper and whine when the cat is around doing such hazardous to his health things, like sleeping on the couch. If he's in his crate and the cat is around he whines and then growls we suspect out of some sort of fear aggression response. We've made his crate as cozy as possible and even give him treats when he's in there (and the cat is not around) to foster the concept 'this is your happy place.' Lately he seems to be turning his nose up at it and fighting it probably because he's understanding now that it means he'll be in there for many hours (overnight.) He is/was crate trained when we picked him up. When he gets spooked by the sleeping cat he whines and gets as close to us as he can. We wonder if his fear of the cat and his inability to curl up next to us when he's in his crate are causing him to growl at the cat out of a fear aggression response. It's getting old. Every 5 minutes at night we have to get out of the bed as soon as we hear him growling and correct him. We don't coddle him when he whines but we don't want to let the aggressive behavior go unchecked. Ah Cecil. It's just a cat buddy!