Originally Posted by Nonnie

By paper training, you are ultimately having to toilet train your puppy twice.
In order to encourage your puppy to toilet outside, you could adopt the 20 minute rule. This means putting him out in the garden every 20 minutes or so, as well as straight after feeding, upon waking up, and after play. Make sure you stand outside with him and encourage him to go, and praise him when he does. He needs to understand and learn that outside is that place to go.

As for the whining, he obviously needs to go to the toilet. I used to get up at about 2am to let mine out for a wee, and then again at about 6am, Oscar never messed in the house, Alfie only did on a handful of occassions. He may be finding it distressing to eliminate in his crate, but at his age, he has no choice.
Personally, id get up early and let him outside to go. He obviously needs to, and by whining he is letting you know. You need to realise this sign and act upon it.