open F, "file1" or die "Problem with file1";
open G, "file2" or die "Problem with file2";

@file1 = map { (split /\s+/, $_)[0]; } <F>;
@file2 = map { (split /\s+/, $_)[0]; } <G>;

while ($coord2 = shift @file2) {
    $coord1 = shift @file1;
    push @result, $coord1 - $coord2;
    unshift @file1, $coord1;
}

open H, "> result.txt" or die "Unable to open result.txt";
print H join ("\n", @result);