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There are probably some more sophisticated options for doing permutations using EnergyPlus than the Parametric objects. Search for "parametrics" and you will find a bunch. OpenStudio has a way, jePlus, eppy, etc.

If you really do want to using the Parametric objects, I would suggest that you simply enumerate every combination within each Parametric:SetValueForRun object. So if you have two variable each with three values (1, 2 and 3), you would make the first Parametric:SetValueForRun 1, 1, 1, 2, 2, 2, 3, 3, 3, and the second Parametric:SetValueForRun 1, 2, 3, 1, 2, 3, 1, 2, 3. Crude but effective.