It would help if you could tell us what it's not doing that you think it should be doing but I think the following will clean up the first half of your code.

sub usage {
    print "usage: proggie [-q] [-i] [-force] search replace directory\
+n";
    exit 2;
}
my @args;
my ($interactive,$quiet,$force);
foreach (@ARGV) {
    $interactive++, next if ($_ eq '-i');
    $quiet++, next if ($_ eq '-b');
    $force++, next if ($_ eq '-force');
    usage() if /^-/;
    push @args,$_;
}
usage() if @args != 3;
($search,$replace,$dir) = @args;
[download]

---
print map { my ($m)=1<<hex($_)&11?' ':'';
$m.=substr('AHJPacehklnorstu',hex($_),1) }
split //,'2fde0abe76c36c914586c';
[download]