It could also be dietary. you may want to experiment with different foods and see if you get a more satisfactory toilet. mrwjd is right, sometimes it just stinks. :)
But if it's loose and watery, something isn't right. try cutting down on the wet food if you're using it, and going with a semi-soft dry food. you may want to go with some fresh foods as well, salmon for example. high iron content could help the problem. you can get cheap cuts at your market and it's really not more or less expensive than canned food.
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You have looked into it pretty thoroughly. It's not the kind of thing you just want to accept as "the way it is," but I suppose it could be. If it's dryer, it'll smell less (they don't NEED canned food in their diet; most are better off without) and a cat chow diet helps some. With seven cats on the same diet, though, we have three distinctly different poops:
Our Bengal has a fairly closely related wild ancestor. Her poop has a gamey, wild smell, reminiscent of the cat house at the zoo;
Our sweetest, petite-est little girl produces a horrendous odor that will drive us from the room, and maybe the house. I think one of her daughters is going to grow up with that talent.
The others are regular. However, two of them (the Bengal and the boy) have stinky URINE. The boy was neutered a couple of weeks ago, so that may change, or at least be encountered in fewer places.
This little trip down memory lane is just by way of saying maybe his sh-t just stinks.
It crosses my mind--although I may be a bit paranoid--that this might be why he was homeless when you found him. Not everyone is kind about a cat's idiosyncracies.
MY fantasy is to have, like this couple we know, a port in the wall and, outside, a big, hardware-cloth enclosure with perches and toys and LITTER BOXES! where the cats can take the sun and leave their less cuddly part outside. Some day.