Poor guy--it's a shame he was cooped up in such a small place he learned to circle. So sad.

I don't know that a 1-level place is necessary for him, although stairs having a "side rail" or being rather enclosed might be (given his history of falling, open stairs might not be a good idea. Mine have about 6 inches of a kitty-sized wall down the open side). Spunk, my blind punk, does stairs beautifully, and, since the stairs won't move, once he learns them he'll be set.

If he has light/dark vision, you might be able to set up a communication system with light flicks; otherwise, I'd continue the thump system you've already started. I suspect he'll be a lot better soon; the shelter seems like such a sensory- and exercise-deprived place given his disabilities.

I've found with more severely disabled (and/or more traumatized--Alex fits both) ones that once you "fill the love bucket" they usually become less clingy, more independent, and they usually go on to do normal kitty stuff.