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3000 unmet hours is clearly too many, because that 's almost 35% of the entire year, so obviously something is seriously wrong here. I can't tell from your description the difference between the two models - are they the same building, only one with autosized equipment and the other with capacities specified by the engineer, or is one a reference building w/autosized equipment and the other the candidate building with predefined equipment capacities ? If the former, then you can just compare the autosized capacities to the predefined ones and see how much is the undersizing. If the latter, then you can't compare the capacities (because the building loads are different), but you can bump up the autosized capacities and watch how the number of unmet hours decrease. I'm not certain, but I believe that EnergyPlus allows input for a Sizing Factor to make it easy to do this.
However, before doing any such exploration, make sure that your design calculations are not faulty - (1) Is the DDY file for the same location and how do the design conditions compare to the maxima on the weather file, (2) is the right month being used to calculate the clear sky radiation? (it should be either January or February for Lima, not July or August as typically used for North America).