I'm no expert at all but a friend advised me(!) that the crate should only be big enough for the dog and its bed with no 'paper' area. Dogs normally do not like to soil their beds and so will hold on until they are out of the crate. Worked a treat for us.
This works unless the dog is left with no choice (if they are crated for too long, for instance) which may have been the case in Alfies previous home?
Once they have got into the habit of messing in their crate, then it can be a difficult habit to break - and it sounds as if it may be complicated by a form of separation anxiety......
If he has been given a clean bill of health by a vet and there is no medical reason why he is messing, then perhaps you would both benefit from a one-to-one with a behaviourist? Although it is frustrating, he really isn't being naughty - he just doesn't know the difference