If only the three originals are showing symptoms, and the tank mates are fine, maybe the situation really isn't a disease problem, but instead a genetic problem.
Generations of inbreeding have adversely affected the quality of livebearers, especially
Guppies, but certainly not limited to them. If you've been following the forums, you might have noticed the numerous postings regarding Guppies with deformities, shortened lives, unexplained death, ect.
It sounds like you keep a good tank, practicing a good water management routine. I'm thinking your Mollies decline is more likely related to genetic weakness, leaving them open to whatever pathagen that naturally lives in the aquatic environment.
I don't believe that Levamisole really does that much harm to the benificial bacteria, so treating the tank is not a bad thing.
If you decide to replace the Mollies, try anotber vendor or a commercial breeder. I think things will get better soon.