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...I put him in...
I was wondering about this.

Are you physically putting your dog in the crate? If so, I would work on training your pup to enter the crate voluntarily.

Instead of a toy and and a safe bone, give your dog a doggy pacifier. What's a doggy pacifier? A Kong, stuffed, and frozen with a favorite goodies or portions of his daily meal.

By the time your pup finishes the Kong he may be too tired to whine, and fall asleep. Plus, you'll be associating the crate with something wonderful.

As it stands now, you're likely inadvertently punishing your dog, if you are in fact placing him in there physically. Whether this is the cause of your dog's whining or not, you still want to avoid this.
 

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The problems seem to crop up more if I leave. The BIGGEST problem is in the morning. This morning he started at about 7am. Cried for about an hour, then just went back to sleep. Doesn't seem to be a bladder issue as when I let him out he doesn't rush to eliminate. Wanders around for quite some time before he goes. I'm wondering if this is separation anxiety? I like the Kong idea during the day.
You have to keep in mind that the whining and crying is a learned behavior. When a pup is first born and they lose the comfort and warmth of their mother, what does the pup do? Whine and cry. And for the first 14 days or so, mama dog is “wired” to retrieve the pup upon his distress signal, no matter what. The pup quickly learns that whining and crying = warmth, comfort, and food. Your pup needs to unlearn this behavior. And the simplest way to do that is to not reinforce it, extinguish it…ignore the behavior. The Kong just helps to pacify the pup when he most wants to rehearse the behavior.

This is very normal puppy behavior that with time, consistency, and training it will dissipate
 
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