I ran mcnp5 ip inp=file
i means process the input file, p means plot the geometry in the interactive plotter.
I click on the "Click here or picture or menu" and type "pz 0" to get a cross section through the reactor. Nothing is coloured in, everywhere I click on the plot is cell 99. This strongly suggests an error in the definition of cell 99, the void cell. Without having much time to look into it :5:6 where 5 and 6 are macrobody surfaces "Top reflector" and "Bottom reflector" feels wrong. Defining those reflectors with simple surfaces rather than macrobodies might make defining the void cell easier.