Well, I answered my own question...PortConnectivity is the parameter I was looking for. Here is some code that will "clean up" the input and output ports for a subsystem like that above (assuming input and output port blocks are connected to the subsystem block). Make sure you select the subsystem to clean-up first!
% get the subsystem port handle positions
pc = get_param(gcb,'PortConnectivity');
% distance from the subsystem to the port
offset = 200;
for i = 1:numel(pc)
      % position of port connector
      y = pc(i).Position(2);
      x = pc(i).Position(1);
      % port block handle and size
      if isempty(pc(i).SrcBlock)
          ph = pc(i).DstBlock;
          off = -(offset-50); % asthetics here...related to the width of the port block
      else
          ph = pc(i).SrcBlock;
          off = offset;
      end
      % port block dimmensions
      pp = get_param(ph,'Position');
      w = pp(3)-pp(1);
      h = pp(4)-pp(2);
      % adjust position of port block
      set_param(ph,'Position',[x-off,y-h/2,x-off+w,y+h-h/2]);
  end




