I had a border collie with separation anxiety. We did not use crate training, so you have an extra tool there, but I can tell you that the way we solved her problem was to get her to slowly be comfortable with very short periods of time being left alone.
Here is how it worked for us: we left our dog in the house for the shortest amount of time that it took for her to settle down, and then came back inside. This could start with as little as 5 seconds as you walk out, close the door, and walk right back in, building up time to where the dog doesn't start destructive behavior or barking/whining. If they kick up a fuss, stay outside until you hear signs of them quieting down, then come back in WITHOUT A FUSS (key)... Repeat until the dog is comfortable for hours... way easier said than done but it worked well for us.
The idea is that they need to realize that you are eventually coming back, and they will be just fine on their own - BUT that if they kick up a huge fuss, that doesn't bring you back. If she is upset enough, you could start by just leaving the room where she is crated, and coming back in when she is calm.
Others may have better or different strategies but this is what worked for our neurotic border collie. Since your dog gives you a good indication of how upset she is (howling/barking) I would use this to your advantage: leave the room/house and re-renter immediately when you hear the barking stop. Ignore the barking, reward the quiet behavior, and make sure she knows she's not getting left alone forever. Good luck !