Hello!
The anxiety and fear he went through when he was younger has remained with him here.
I too have a cat who's very affectionate but scared of people until a trust bond is built. It is very difficult. as regards to keeping you up in the night - I put my cat in one room. She's used to this and for a cat who is anxious it's a secure environment for them as well. My cat has stolen my arm chair and sleeps on it for the night with her own blanket etc. For her - this is a secure and safe place for her. You could try the same for your cat - shut him in one room at night - he will then begin to feel safe in that area. At the moment he is obviously anxious and meows for attention to tell him everything is OK - but obviously by kicking him out of the room is just reinforcing his fear and anxiety with people.
As regards to his fear of people - that is a very difficult one to resolve. It's worth bringing in strangers to your cat for a few moments at a time to allow her to get used to dofferent people in that envoroment - introduce her to them slowly - be prepared for him to run around and encourage the person to entice him and then give him a treat or affection when he comes up near there hand etc.
You could definately try a Feliway adaptor if you haven't tried this already. It's a plug in that you put in your house that realease a natural happy phermone into the atmosphere that only affects your cat. When your cat rubs against you he is releasing this pheremone too. It's design is to calm and help battle cats with fear and anxiety problems.
Also - if you havn't already - make like a 'safe haven' place for him to go to when he is in a panic i.e a box in an open wardrobe, a rug on the bed in a spare room -again, it's somewhere he feels safe as is then more likely to allow people near him. Put a Feliway adaptor in the room he is in at night and his 'safe have' areas.
Does this all make sense?? They are simply litle tips for you to try. You can get the Feliway product at a discounted price from entirely pets.com. Just Click here.