Cats not peeing in litter box. I need help before its to late :(

So i recently adopted a 3 year old cat, Niles. For the first 2 months went really well. Getting him used to the two other cats we have in the house. One of those cats (jasper) is a five year old cat I found outside as a kitten. He is friendly to all the animals in the house and spends most his time outside where he does all his bathroom business. The other cat or kitten rather (Murphy) is around 8 months old. She has a personality and originally wasn't to fond of the new cat but she came around and doesn't mind Niles so much now.

Within the last two weeks Niles has stopped peeing in his litter box. Still poops but chooses different areas around the house to pee. Originally we had the main litter in a closet in the laundry room but moved it believing the kitten Murphy was cornering Niles in making it very stressful to use. After moving it Niles started peeing in the box again. Unfortunately after a few days he stopped again. After this being a consistent problem the kitten has now stopped using the litter box too. Im sure she's taking it as a territory issue.

In the house there are three litter boxes. One that is used by the kitten only. The box that I have been mostly talking about is used by Niles to poop and occasionally by the kitten possibly but not sure. Another box isn't being used by either cat.

Niles has been tested for sickness but seems to be perfectly fine. There haven't been any changes in the litter. Any accident is cleaned with recommended cleaning products to fully kill the smell. So I imagine the only reason I see this happening is between the two cats. I ask sor any solution that might help my situation. The home owner can't take the smell and the possible damage that can be done to the house. The final solution would be to return the cat back to foster care. Which would break my heart please help

Your new cat may be peeing outside the litter box because it's scared, still fairly new, or trying to mark it's territory.

Other major reasons could be a UTI but as you said the vet said your cat is fine. It's very important to make sure you clean the area properly because if the cat smells the slightest bit of urine it may pee there again, but if you've been keeping up on that...you may want to try getting another litter box and putting it somewhere more private where it feels safer.

Are you cleaning your boxes frequently? What kind of litter are you using?

Can you try separating your cats for a time? It sounds like they need some space to regain confidence. Do you play with them together? That could help bond them.

One thing you haven't tried is cat attract litter. It helps to draw cats to the box. And how often are you cleaning the boxes?

Are all the litter boxes covered?  If they are I would suggest to try taking the cover off one of the litter boxes.  Sometimes if there are issues between the cats over litter box use taking the cover off provides extra escape routes for a cat that my be getting cornered in the litter box.

I also 2nd the suggestion on using cat attract. 

Also make sure the liter box is being cleaned enough.  Some cats are really fussy about their litter box being cleaned right away.