I don't think it's that you gave him too much freedom, but more that he is not so happy in the crate as you thought. I'm going to attach a guide to crate training which is quite a long read, but is the best one I have seen - it was written by Emma Judson who is a behaviourist who specialises in separation anxiety.
Does he stop the barking when he can see you? If you are sleeping right by the crate, does it have to be shut - would you hear him anyway if he were to move? D you actually need a crate at all?
But - please don't leave him to cry. Apart from the problem for your neighbours, the dogs that stop don't do it because they suddenly realise that everything is ok, they do it because they have given up hope that you will come to help them. It is an extreme example but in trauma victims it is the silent ones who are most damaged. This article explains more.
www.simplybehaviour.com
Does he stop the barking when he can see you? If you are sleeping right by the crate, does it have to be shut - would you hear him anyway if he were to move? D you actually need a crate at all?

But - please don't leave him to cry. Apart from the problem for your neighbours, the dogs that stop don't do it because they suddenly realise that everything is ok, they do it because they have given up hope that you will come to help them. It is an extreme example but in trauma victims it is the silent ones who are most damaged. This article explains more.

Self Soothing & Cry It Out Are Neurologically Damaging Here Is Why - Simply Behaviour - Applied Behaviour Analysis
The mechanisms that occur when ANY animal feels stress or anxiety is conserved across the way the nervous system responds. We are looking at the limbic system and basically under the hat we are all the same (according to Panksepp et al) This is why we use Rat models to draw conclusions about...
