Squirt has been under my vet's care since we adopted him on Aug 3. It wasn't the shelter, but the adoption center at a very well known national pet supply chainstore that used the windex. As soon as the rescue workers found out Squirt was sick, they immediately pulled all of the cats from the adoption center, had them put under vet care, and sanitized everything (thinking it was a bad viral infection). The shelter manager saw the bottle of Windex, and that's how she found out it was being used to clean the cages. When it was brought to the attention of the manager at this pet supply superstore, the manager rolled her eyes and said "not my problem". I am writing a letter of complaint to the district office and requesting that they at least help cover the vet bills.
Squirt has been improving thankfully. He is now eating on his own, and is more active. He still spends most of his time sleeping and he has a discharge from his nose, but the vet has him on an antibiotic and a decongestant. We are hoping he will make a full recovery.
He is still not urinating in his litter box, so we're concerned about that as well. However, if he has some sort of chronic permanent issue from the windex exposure that is causing him to not use his litterbox properly, we will diaper him or figure something out. I'm not willing to give up on him. I would be suprised if it was from a UTI as he has been on antibiotics for almost 2 weeks now.
I also use all non-toxic cleaners around the house to clean, as we have birds as well as dogs and cats. Murphy's oil soap is awesome stuff. I use it to bathe the dogs with as well as my cabinets and wood furniture, and have bathed the kittens in it since it is a non-toxic cleaner.
When I said I was calling the vet first thing in the morning, I meant to tell him about the windex exposure. Again, he has been under my vet's care since Aug 3, and has been seen 4 times since then. We have been watching him very closely. I want to thank everyone here for their concern and advice. I am wondering about long term affects for poor Squirt and what his prognosis may be. My vet said we will treat him symptomatically, and that his odds of making a complete recovery are high. This is my first time dealing with a situation like this, so I'm pretty worried.