My cat, a former feral, had idiopathic cystitis in the first year he was with me. Again, stress was the cause (or sensitivity to it). My vet wanted to put Oscar on anti-depressants, but I wanted to try Feliway first. Feliway is a spray that contains the 'happy place' pheromones that cats give off when they rub their heads against something they like.

You might try a short course of mild antidepressants and see if the situation improves. That might help the litterbox issues as well.

HUGS - how heartbreaking. I know you will find an answer from someone here.