I suggest you check elsewhere in this very thread to see something that will likely be very fast while still being very easy to write. [ I've really grown to like sorting replies by reputation (see your User Settings) ]

Update: Though, if you want to ignore blank lines, then that won't work. So here:

my( $lineA, $lineB );
while( 1 ) {
    $lineA= do { while(<FILE1>){ last if /\S/ }; $_ };
    $lineB= do { while(<FILE2>){ last if /\S/ }; $_ };
    last   if  ! defined $lineA  ||  ! defined $lineB;
    for( $lineA, $lineB ) {
        s/\s+/ /g;
        s/^ //;
        s/ $//;
        $_= lc $_;
    }
    last   if  $lineA ne $lineB;
}
if(  defined($lineA)  ||  defined($lineB)  ) {
   warn "The files are different!\n";
}
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