The orientation of the pressure vessels does not matter. Typically, in larger systems, the orientation is horizontal. This is really for removal/replacement of the membranes, and not a hydraulic issue. Your water does not seem bad at all, with the turbidity and SDI cleaned up a bit the RO...
OK ProjEng, let's start from the beginning... you say this is city water, I assumed it was already treated to potable standards, but you just wants to reduce the TDS down further. What exactly is the source water quality like in terms of TDS, suspended solids, etc. The ultrafilter you mentioned...
If they ran straight City water through the Plant w/o removing the chlorine, then the membranes are swiss cheese (unless the membranes were CA rather than polyamid). Basically you are looking at two treatments; surface water and RO. With the flowrates you mentioned (6MGD to 9MGD) you could...