Have you considered using the seek function. This test shows reading the first 3 lines off of STDIN, then seeking back to the beginning of STDIN and then iterating through the handle normally.

my $c=0;
while($c<3){
  my $l=<STDIN>;
  print "## $c ## $l";
  $c++;
}
seek(STDIN,0,0);
while(<STDIN>){
  print ".... $_";
}
[download]

There is probably some annoying OS trickery that would cause this "seek on STDIN" technique to fail on certain OSes and under certain conditions, but it tested properly where I wrote it. I hope you are as lucky.

Another idea would be build a "rewindable filehandle" with either a tied filehandle or a subclass of the IO::File module that would hold a "back buffer" and have a rewind function. It's too late on a friday for me to come up with any more details of exactly how this would be done, but I think it is doable. Of course, this would only be necessary if the seek method doesn't work for you.

There is always the less-elegant solution of dumping all of STDIN out to a temp file, opening the temp file, grabbing the first n lines for your pre-processing, closing/reopening (or seeking back to BOF) the tempfile, and passing that handle to MIME::Parser. This is easier to code than the advanced approaches I mentioned above, but will really increase disk IO and just feels icky.