Figured it out finally, had to do a loop, inside of a loop, which id never done before. I was doing it in a loop, in a loop, in a loop... but i changed it
I would love to learn how to do sub routines
Anyway here is the final working code as of now.

use File::Path (make_path, rmtree);
use Digest::MD5;
use File::Slurp;

rmtree 'extracted';
open (my $infile, '<', $ARGV[0]) or die "cannot open file: $!";
binmode ($infile);
make_path ('./extracted');#or die "Failed to create Direcotry: $!";

my $curpos = '';
my $fileLocation = '';
my $fileSize = '';
my $fileName = '';
my $file ='';
my $chunk = '';
my $exit = '';

#GET File Location, File Size, File Name and write to file
seek ($infile, 0x10, 0);
until ($exit){
    read ($infile, $fileLocation, 0x08);
    read ($infile, $fileSize, 0x08);
    read ($infile, $fileName, 0x20);
    
        if ($fileLocation =~ 'SCE'){
        last;
        }
        
        $fileLocation =~ s/(.)/sprintf("%02x",ord($1))/eg;
        $fileSize =~ s/(.)/sprintf("%02x",ord($1))/eg;
        $fileName =~ s/\0+$//;
        
        if ($fileLocation =~ 'ffffffffffffffff'){
        last;
        }
        
 open($file, '>', "extracted/$fileName") or die "Cannot open $fileName
+ $!";
    binmode($file);
    sysseek ($infile, hex($fileLocation), 0);
    sysread ($infile, $chunk, hex($fileSize));
    syswrite ($file, $chunk);
            
$fileLocation = '';
$fileSize = '';            
};

my $dirname = "extracted";


open (my $sdk, '<', "extracted/sdk_version") or die "cannot open sdk_v
+ersion: $!";
    seek ($sdk, 0x00, 0);
    read ($sdk, $buf, 0x03);

# my@fn;
# my @hash;
my @md5s = read_file 'C:/md5';
chomp @hash;
chomp @md5s;
# open (my $md5file, '>>', 'C:/md5');


foreach my $file (<$dirname/*>) {
    next if -d $file;
    open( my $FILE, $file );
    binmode($FILE);
    
$file =~ s{.*/}{};
     
    my $md5 = Digest::MD5->new->addfile($FILE)->hexdigest;
    push (@hash, $md5);
     
    # syswrite $md5file, "$md5\n";
}

foreach  $md5s (@hash) {
                foreach  $md5table (@md5s) {
                        if($md5s ~~ $md5table) {
                        print "$md5s ", "$buf ", "success\n";
        }
    }
}
[download]

file to reference with

I dont like a few things about the foreach loop that gets the md5 tho because i cannot print the filename with the md5 checksum.
i will probably end up rewriting this lol.
thanks for all your help :)

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