When you first posted November 2016), the assumption was that this was a surface water application because of the high SDI. The 2 stage filter was proposed for surface water filtration.
On January 14, you disclosed that this was a well application. Wells should not have suspended solids. The 2 stage filter is not appropriate for well applications.
At this point, it should be obvious that the reaction times for iron, manganese, and hydrogen sulfide are very long. Air oxidation of hydrogen sulfide will take several hours while the water transit time through the filters is only in minutes. That means the air oxidation reaction will be completed after the water has passed through the filters so you may actual experience have higher suspended solids in the effluent of the filter than in the inlet to the filters.
However, it is best not to jump directly into solutions without a complete understanding of what the problem is. You really need to determine if it is hydrogen sulfide, iron, or a combination of both.
pH, iron, manganese, and hydrogen sulfide concentrations should be determined in the field since these parameters are not stable.
Water samples must be tested on-site, or immediately stabilized for laboratory analysis. Sample bottles with stabilizing chemicals should be obtained from the laboratory that does the analysis. Careful sampling according to laboratory recommendations is critical to ensure accurate and reliable results. In general, the requirements will involve delivery of a refrigerated sample within 48 hours of collection. Sulfide concentrations are reported by laboratories in units of milligrams per liter (mg/l) or parts per million (ppm).
What does the water treatment company have to say in this matter? It seems that they supplied you with a defective treatment scheme.