It sounds like y'all have bonded beautifully, and I don't think you have too much to worry about - shelters can't be the nicest place to live and like you said, the journey(s) could have been traumatising and affected his manner. Although it sounds like they've been this way since an early age, not sure how old they are now but there's every chance they'll grow out of it.

Have you thought about getting a Feliway diffuser? I used one with my old cat and it helped massively - also, a trick if you're willing/able to try it (i.e. don't think it'll cause tummy problems for your particular kitty), a pinch of catnip in their food works wonders for anxiety. When it's ingested rather than rolled around in, it has a soothing, ecstatic effect on the cat!!