You mentioned a "series" of ASCII files, so I assume that we have one message per file. If so, how about the following? I'm using a hash, but only for convenience. Also, note that this is simply a rewriting of your inner while loop. I didn't add the rest as I was going for clarity.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %message;
while (defined (my $line = <DATA>)) {
    chomp $line;
    my ($field,$value) = $line =~ /^<([A-Z]+)>\s*(.*)/;

    $message{$field} = $value;

    # assumes message is last item in file and doesn't
    # start on same line as MESSAGE key
    if ('MESSAGE' eq $field) {
        $message{$field} = do { local $/; <DATA> };
    }
}

print Dumper \%message;

__DATA__
<SENDER> Sender Name
<TO> To list
<FROM> User Name
<MESSAGE>
Text text text tex
[download]

Cheers,
Ovid

New address of my CGI Course.