Hi Matt, maybe try just sitting at the door with him,don't encourage him to go out,allow him to realise that he can and assure him that he's safe if he does(assuming he is)
The cat that you've had probs with,could be a problem for your lad either on sight or through the other cats smell?And as you say it's very early days yet and you don't know what his past was,slowly,slowly as the saying goes-he and you will get there