Why not let Perl do the buffering for you. read and write are buffered (unlike sysread and syswrite).
while (my $bufsize = read(INFILE, my $eight_byte_chunk, 8)) {
...[ Add padding ]...
...[ Encrypt ]...
...[ Merge with IV ]...
...[ Compute new IV ]...
write(OUTFILE, $eight_byte_chunk, 8);
}
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