Hey there Maybe,
Those are flower and daughter plant buds coming from your swords. At this point it's in your best interest to trim those off so the plant puts all of its energy into growing rather than making babies.
As for the filter system, detailed photos will help me see what the flow is like in the various parts of the sump(s) which will let me figure out how to get actual filtration going. Socks alone aren't sufficient filtration for a freshwater system since they don't have the rock to act as biological filtration or a skimmer to deal with dissolved pollutants.