We adopted Angus and Finn at around 8 weeks old (they're 4 now), so we've had them for almost their entire lives. Angus and Finn have a good relationship, they often sleep together and groom each other.
We do have a dog, Skylar, who is a relatively new addition (we've had her for1.5 yrs). For the most part the dog and cats ignore each other, but if the cats start to play and chase, Skylar tries to join in, which sends the cats running for the highest point in the room. This could be part of the problem, and we do try to prevent Skylar's chase instinct.
SCM, I quickly read through the article you provided and I see some things that I can implement; change the type of litter, perhaps be more vigilant with litter cleanliness (we're pretty good, but I guess we can always be better). Find some better games and toys for Angus. I also think I may put the baby gate up again so that the cats can have a dedicated area of the house away from the dog.
Unfortunately due to the type of townhouse we have (no backyard) we can't build an enclosure for him. I went out and bought a new harness today and may have to spend more time outside with him.
The vet suggested some meds (antidepressants, I think). But according to that article, the effectiveness is hit or miss and can cause worsening in some cases.
This may be a horrible thing, but it was also suggested to me at the vet's office by one of the techs. Put Angus in a bathroom with food water and litter for a week so he's forced to use the litterbox. As of a few hours ago, I've done this. Perhaps doing this just when we're not home would be better? I'm still very angry right now and can't really stand the sight of him, and he's probably safer in there right now
as I'm cleaning the mess.