First off, its great that you have rescued him and have helped him recover =)!
Sitting near the cage everyday is going to help make him less sensitive towards the cage proximity. You will need to work on this with small stages, getting closer and closer to the cage. Much like how you train them to accept handling really.
Clipping him wasnt a good idea in my opinion. It makes birds less sure of themself and can lead to depression. The idea that clipping would be a good thing is quite old, and can be found in much literature still, but its an old practise, and by many considered a bad practise.
It also doesnt help that your others birds are flighted, because if there's a fight, he alone now cant fly away. I would let him regrow his flight feathers, and stop clipping.
Keep working with him, it sounds to me like you really care about him

and I am sure you will succeed in creating a strong bond between the two of you =)!
Also, dont be discouraged by the fact that he's an aviary bird. One of mine is, and he's the sweetest thing ever!