When you read your input files, you intentionally disregard the header lines because they do not match your regex (
/\s*(\d+)\s*(\d+\.\d+)/). Because of that, I presume you know ahead of time what the headers should be. Why not just print them out before your print loop?
print "Merged output\n";
print "Distance Fuel_Consumption_Curr Fuel_Consumption_Baseline1\n";
On a side note,
Text::Table is handy for printing simple text tables.