Your sons' is an easy fix. Close his door. Cat can't get in; cat can't wake him up.
Did the vet take a urine sample? You don't have to take the cat in for another visit. You just need his pee. If you can use Nosorb (from the vets) to get a urine sample, put it in a sterilized bottle and get it to the vets asap for testing they can see if he has crystals in his urine. The longer it sits before going to the vets the more crystals develop which is why I say asap. If it can't get there immediately store it in the fridge. Him peeing outside of the box is a sign that something is wrong. Was there blood drawn at the vet?
Is there a possibility that there is a strange cat around? He could be peeing for territorial reasons. You may not see the cat but he may. That could also be a cause for his crying at night. Cats are, after all, nocturnal. Is there a possibility his litter had not been cleaned for a while and he was rebelling against using it?
Do you live in an apartment or a house? Is there a room you can put him in at night away from the bedrooms and close the door. Give him a litter box, his scratch post, lots of toys to play with, the other kitty, and his food and water. Play with him and tucker him out before bed. I know you said he doesn't play with you but I have yet to see a cat that will not chase a string that is being dragged on the floor or bat at a toy that is being dangled. There are tons of those fishing pole type toys at the dollar stores that cats just love.
Assumptions do nothing but make an ass out of u and me.
We can stick our heads in the sand for only so long before it starts choking us. Face it folks. The pet population is bad ALL OVER THE WORLD!