I think that you might want to give up on the crate, at least for a little while. If he whines and howls when he is in the crate, he is not happy in there. The point of putting a dog in a crate is that they go to their crate to feel safe.
Don't leave your dog in the crate too long. A dog that’s crated day and night doesn't get enough exercise or human interaction and can become depressed or anxious. You may have to change your schedule, hire a pet sitter, or take your dog to a doggie daycare facility to reduce the amount of time he must spend in his crate every day.
Limiting his time in a crate may help him stop associating his crate with a bathroom.
The source I used has step-by-step instructions on how to crate train a dog. I'm not saying you messed up, but perhaps you may have been over eager and gone too fast for your dog.
There may also be another reason your dog is whining.
Whining. If your dog whines or cries while in the crate at night, it may be difficult to decide whether he's whining to be let out of the crate, or whether he needs to be let outside to eliminate. If you've followed the training procedures outlined above, then your dog hasn't been rewarded for whining in the past by being released from his crate. If that is the case, try to ignore the whining. If your dog is just testing you, he'll probably stop whining soon. Yelling at him or pounding on the crate will only make things worse.
If the whining continues after you've ignored him for several minutes, use the phrase he associates with going outside to eliminate. If he responds and becomes excited, take him outside. This should be a trip with a purpose, not play time. If you're convinced that your dog doesn't need to eliminate, the best response is to ignore him until he stops whining. Don't give in; if you do, you'll teach your dog to whine loud and long to get what he wants. If you've progressed gradually through the training steps and haven't done too much too fast, you'll be less likely to encounter this problem. If the problem becomes unmanageable, you may need to start the crate training process over again.
Perhaps starting over with the crate training will help your dog and you solve this problem.