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I've had a lot of cats, and most of them have peed outside the box at times. The worst was Minnie--a beautiful but neurotic and overweight beast. When she lived in a house with three other cats, she stopped using the litter box, and nothing helped. I moved into an apartment with just her, and still she did it. Ruined a very cheap and ugly couch that way. I finally took her to the vet when I noticed her peeing clear, odorless liquid. She got antibiotics and some other treatment, special food, and instructions to lose weight. She lost too much weight and went into fatty liver syndrome, requiring almost two months of forcefeeding to recover. After she recovered, she used the box faithfully. Except that in the mean time I had gotten her a bigger box, because at 20lbs she had trouble using the smaller one. The new box also had lower sides. Getting a second cat never upset her.
So, it was either the box or her health or her weight or a combination of those. Given that in the house the box never changed, I think us gaining two more cats upset her, but I think her weight gain also made it harder to use the box without positioning herself over the other cats' business. Plus, I think her weight was partly the result and cause of some health issues.
Bottom line, she was not using the box because she was miserable. It wasn't one solution, it was several, and I had to improve her comfort level with a bigger box, diet, weight loss, and medical treatment, and that eventually worked.
If you know much about his prior history, see what's changed. Has he gained weight? Are you feeding him the right food? I tried EVO with my cats and they weren't happy with it. I use Halo now. IIRC, EVO is high in protein, and with your kitty's weight (no matter his size, that's overweight for a cat), he may be having kidney problems. Maybe not enough to show, but enough to make him uncomfortable, and that combined with less than perfect social conditions (maybe), he's just unhappy and not worried about tidiness or rules. High protein would make that worse. Just imagine yourself in that shape--maybe a bit of pain, inability to get comfortable, overwhelmed by emotional changes... Eventually you get less tidy. Housekeeping slips. Same with a cat.
Don't worry about him bonding more with the females than the males. He probably was alpha cat before. Men aren't a threat, but they aren't who he bonds with. If he's not being aggressive to them, they probably aren't a problem for him, though the change in his status may contribute to his box habits.
I've had a lot of cats, and only one I couldn't box train. She was a feral my kids rescued, along with her kittens. Even with her own room and box, she wouldn't use the box. I think for her it was misery over not being outside. The box smelled like captivity to her. That doesn't sound like the issue with yours. We never could train her, though we only kept her a couple of months.
So in short I'd get another vet check, put him on a diet, make sure his box and litter type is comfortable with him, and maybe worry about the food. Don't isolate him and don't keep changing his rules. It doesn't sound the other cats are a problem. And give him time. You can also try polluting the spots he uses. My vet recommended a slight bleach mixture to keep him away, others have recommended bitter herbs. Make the other spots unpleasant for him, make the litter box more pleasant.
Lots of words. Maybe some of them will help.
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