Uh...you are going to need a much bigger tank for them. Are you aware Mollies can grow to 4-6"? So if you can, get at least a 10 gallon, 15+ is much better. What kind of Mollies do you have though? Balloon, regular, Sailfin?
And It sounds like the female is getting stressed, which makes her more prone to disease. See, with male Livebearers, they want to breed all the time. When they eat, when you do a water change, when you watch them...all the time.

Therefore, the female will get pretty stressed out, by having the male chase her constantly. And in that size of a tank, she can't get away from it. So, what I would recommend you do, is upgrade the tank size to at least a 15, and get at least one more female. That way, each female will have some rest period, and not have to worry about the male chasing her all the time.
It's good you are adding salt though, that usually helps them out.
I wish you the best of luck!
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