as for your code

while( $_ =  <EMAIL> ) {
    if (        /^Message-Id:/
         ||     /^Content-Type:/
         ||     /^Content-Disposition:/
         ||     /^Content-Transfer/
         ||     /^X-[-\w]*:/
         ||     /^Status: RO/
         ||     /^Mime-Version:/ ) {
        next;
    }
    .
    .
    .
}
[download]

I'd put the things you want to match the message against into an array and go through that:

@array=qw (Message-ID:
           Content-Type:
           Content-Disposition:
           and_so_on...
);
LINE: while( $_ =  <EMAIL> ) {
    foreach $header (@array) {
        next LINE if /^$header/;
    }
    .
    .
    .
}
[download]

The code is untested, so I'm not sure it works... but I hope it helps nevertheless.

BrotherAde