1a > the properties you input into the engineering database are based on your sample, flow simulation will scale it up based on the model that you actually use.
1b > can you elaborate on what you want tortuosity and permeability to do? the porous medium properties are well defined in the help if you want to look into how they work
2 > do not believe this is possible with flow simualtion. flow simualtion does not handle mixing of different species or the "chemical-type" diffusion i think you're looking for, have you seen this done in other CFD?