The feliway isn't a sudden thing, it can take time to reasure a cat and I guess that's why they have the plug in last for 4 weeks feature, and some people use them almost continuously if they have cats that get illnesses triggered by anxiety like cysitis or feline herpese (expensive but effective). It feels interesting that she is choosing to stay in the safetly of the crate and resting in the litter, esp given she wouldn't toilet in her litter at the start. Much as it is frustrating and you want to offer her comfort it seems she finds the crate and litter reassuring for some reason. Is she feeding in the crate too or will she come out to eat? It is maybe like introducing a cat to a new home where it has to be very gradual and that her companion not being there has left her feeling disoriented and confused, as well as maybe depressed? I take it there is no sign of any other changes to indicate any physical illness still?