I am a bit confused with your statement "The dates in Inputfile2 are layed out exactly like the way I have put them they dont have a variable assigned to them." If there isn't a variable associated then how do they exist in SAS? You would probably be better off transforming the data from inputfile2 to have variables County, Location, SchoolCode, ComparisonDate (the column headings), and the values in those columns as DatesAbsent. This is likely easy once the date issue is clarified.
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