my $md5chksum = &calcMD5( $save_file );
[download]

How do you calculate MD5? You don't show that subroutine. Are you aware that Digest::MD5 is CORE?

You should also be aware that invoking subroutines with the & sigil shows different behavior than calling a subroutine without it -- see Prototypes in perlsub. It can also interfere with optimization -- see Constant Functions in the same document.

               my $cmd = "rm $save_file";
#               `$cmd`;
[download]

Rather than invoking a system command, you can use unlink.

            open ( MD5, '+>>', $md5File )
               || &loggingError("Couldn't open md5 file ($md5File) for
+ reading : $!");

            $md5row = <MD5>;
            close( MD5 );
[download]

It's generally good practice to use lexical file handles, since barewords are globals. Search for "lexical" in open.