Since the file is binary, you don't want to be reading it with angle brackets (<>) because you don't know if there are ANY new line characters in the part of the file after the headers. Use sysread, and keep adding to the buffer, until you see the end of headers marker. Then just remove the headers with a regex, and cycle through syswrite and sysread (with the appropriate sized buffer, like 16 or 64 K) until you reach the end of file.

Update: here is the example code:

my $buf="";

#append to buffer until headers are found and removed

while (!($buf=~s/^.*?#### end_ascii_header\n//)) {
  sysread(INP,$buf,1024,length($buf)); 
}

syswrite(OUT,$buf,$length($buf));

#copy the rest of the file
while (sysread(INP,$buf,16384)) {
  syswrite(OUT,$buf,length($buf));
}
[download]

P.s. In production code, checking the return values of syswrite would be prudent.