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`CreateInput`

      65       if ($What == 1) {
      66           print "Creating DIR: ",$InputDIR1.$NextOut,"\n";
      67           $I = mkdir ($InputDIR1.$NextOut,0777);
      68       } else {
      69           print "Creating DIR: ",$InputDIR2.$NextOut,"\n";
      70           $I = mkdir ($InputDIR2.$NextOut,0777);
      71       }

Why one function? Why not two functions?
Or no functions?
This if-else block is the perfect example of why you should Avoid families of variable names
With an array, it becomes:

           print "Creating DIR: ",$InputDIR[$What].$NextOut,"\n";
           $I = mkdir ($InputDIR[$What].$NextOut,0777);

Five lines become two