My money is on insufficient fixing, but that doesn't say all that much when it comes to salt prints. It can be due to the fixing itself being inadequate, the paper being impossible to clear effectively or the chemistry not being optimal. I would recommend the following in your case:
* Your fixing is really borderline inadequate as it is. I'd go for 2x 5 minutes in 10% sod.thio., using *fresh* fixer for the second round. Personally I vastly prefer rapid fixer (diluted ca. 1+20) used one shot. It doesn't take much. But rapid fixer is much more effective and rapid (no surprise!) than old-fashioned sodium thiosulfate.
* Your wash step is equally dangerously short. Wash for at least twice as long as you're doing presently.
* Ammonium ions are notorious for causing fog in silver-based printing. Give plain old sodium chloride a try; it works really well.
* I'm not sure you need quite as much citric acid as you're using; I tend to use a bit less; probably half it. But you have a very heavy silver nitrate solution as well. For comparison, for a 4x5" image area print I use about 0.75ml of 11% silver nitrate with 2 drops of 10% citric acid added to it. I do use a coating rod/puddle pusher as I never got satisfactory results with a brush. In my mind, you'd want to lay down the absolute minimum amount of silver that will still easily reach dmax - but not more than that. At some point, additional silver won't contribute to image formation, whereas it will actually contribute to fog, place a burden on fixation etc.
* I assume, but it's not clear from your description, that you wash with slightly acidified water - if not, make sure to do so. It only takes a few grains of citric acid to sufficiently acidify a pint of tap water for this. Half a teaspoon to a quart of water is more than enough, but does really help clear the prints, partly because the citric acid seems to act as a chelating agent, effectively 'capturing' unexposed silver from the paper and dissolving it.
* Try a different paper. Salted paper prints are finicky when it comes to paper choice. Some papers will simply never clear.
* If all else fails...accept the situation and matte over the stains. To be honest, I've seen stains much worse than yours, although photos are always a bit tricky to judge this kind of thing from.
One last thing - in order to establish the effectiveness of your procedures, I would really recommend making some prints with a clear border, which requires masking. If the masked whites come out clear and stay clear as the print ages, you know your processing is good. And I'd say it's the *only* way to know if it's good! I never knew if my processing was somewhat reasonable (it wasn't!) before I started masking out my print margins.