Children can be a huge stress factor in cats, especially young ones who are loud and boisterous at times. The fact that he goes in your son's room may indicate a dislike for something in that room. There are so many things that could be causing this and only your kitty knows what that is. Owners can only guess and then attempt to rectify the situation the best we can.
I'm hoping the bathroom you're confining him to is huge because cats do not like food near a litter box, just like you wouldn't want to eat your dinner next to the toilet. Sometimes you have to put yourself in the kitty's place. If the bathroom is a standard size, then you have too much going on for him in a very small space. Perhaps he doesn't like to be locked up there at night. Does he have a bed in there or does he have to sleep on the floor?
There is something distasteful, in his eyes, with the litter boxes. One is covered, one is not. They both need to be either covered or uncovered, depending on the cat's preference.
The fact that you've had cats previously who have peed outside the litter box is a telling sign as well. All areas must be cleaned immediately and completely. You may not be able to smell the residue of urine, but a cat's smell is 14 times better than ours, and they can smell it.
I've never had a cat with a UTI, so I don't know if they behave any differently. The only way to tell is a visit to the vet. If it's not medical, then it's behavioral and that's something you deal with bit by bit. The kitty is not happy about something when it comes time to go to the bathroom. And you don't want to go moving litter boxes around to different places in the house as that only confuses the cat, which is why I mentioned adding a couple. Since your home is small and you don't have room for any more, you'll have to solve the problem with the two boxes that you have. There are cat litters that supposedly attract the cat, so you may want to try something different in the boxes.
When all else fails, google "cat not using litter box" and read what has worked for other people. I know this is an exasperating problem and I really hope you find the solution soon.
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