Well, I got this working, although I there are several things that don't seem to work they way they should. Short summary: Must use perl function private_encrypt() instead of sign(), even though, to generate the same signature, the command-line tool must use -sign. Must use the SHA1 digest generated by command-line tool, since $rsa_priv->use_sha1_hash() has no effect on private_encrypt().

I don't understand this well enough to say that these are bugs. More comments are in the code in case anyone is interested.

Here are my revised commands/code and working results, starting with the command-line:

###############################################################
# Create a private key
jk$ openssl genrsa -out Test248.private.pem
Generating RSA private key, 512 bit long modulus
.........++++++++++++
.............++++++++++++
e is 65537 (0x10001)

# Create SHA1 digest of message "Bonehead".
# The, write digest to file for later use by perl script.
# Finally, sign the digest using the key in file Test248.private.pem
# and PKCS padding.  Why PKCS?  See note [1].
echo -n "Bonehead" > clearMsg.txt
openssl dgst -sha1 -binary -out msgDigest clearMsg.txt
cat msgDigest | openssl rsautl -pkcs -sign -inkey Test248.private.pem - hexdump

0000 - 8a c6 56 19 97 f5 e7 16-20 30 f2 2f 0e af 7c 28
0010 - df 9d cd 5a 0e b0 11 c1-cc bb f2 3b 03 87 f0 96
0020 - 0d ce b4 55 dc 69 81 bc-30 40 75 9d 74 b8 b7 bd
0030 - 3b 15 a0 5d c2 db ab 9a-8d d3 f2 4b 77 e1 e9 a1
##############################################################

Now create the same signature using a Crypt::OpenSSL in Perl:

##############################################################
#!/usr/local/bin/perl -w

use strict ;
use warnings ;

use Crypt::OpenSSL::Random ;
use Crypt::OpenSSL::RSA ;

# Read in key from file
my $private_key_string = "" ;
my $key_path = "/Users/jk/Documents/SheepSystems/Keys/ Test248.private.pem" ;
open (KEY_FILE, $key_path) ;
while (my $line = <KEY_FILE>) {
    $private_key_string .= $line ;
}
close(KEY_FILE);
print "Read key from file:\n$private_key_string\n" ;

my $rsa_priv = Crypt::OpenSSL::RSA- >new_private_key($private_key_string);

$rsa_priv->use_pkcs1_padding() ;
=com
Padding is a big mystery.
The above affects encrypting with the private key
but does not affect signature generation.  As a matter of
fact, it is necessary when using the private_encrypt()
method.  Without the above, private_encrypt() will fail
with error.  I believe the problem is that OpenSSL does not
support oaep padding for signing, which is what you're
doing when you encrypt with the private key, despite doc to
the contrary.  See note [1].
=cut


# $rsa_priv->use_sha1_hash() ;
# The above has no effect on the output of the
# private_encrypt() method.  So, I don't use it.

my $output ;
my $outputHex ;


my $msgDigest ;
my $msgDigest_path = "/Users/jk/Documents/SheepSystems/Keys/msgDigest" ;
open (MSG_DIGEST_FH, $msgDigest_path) ;
# SHA1 Digest is 20 bytes...
read MSG_DIGEST_FH, $msgDigest, 20 ;
close(MSG_DIGEST_FH) ;
$output = $rsa_priv->private_encrypt($msgDigest);
# If you use sign() instead of private_encrypt()
# above you get a different output.  This does not make sense
# to me because I thought that signing was the same as
# encrypting with the private key.
$outputHex = showHex($output) ;
print "privately encrypted msgDigest:\n$outputHex\n" ;

# sub showHex is shown at the bottom of this message
##############################################################

Running the above script, I get this:

##############################################################
Read key from file:
-----BEGIN RSA PRIVATE KEY-----
MIIBOgIBAAJBALE2d5DpKbYxfIqv+6jYnW6DDvDyJFCdQt+s432GQsy8+ymL9DOR
mPcRQfk1jas1pqtsy+GGUlYd4R1kxbBZb4UCAwEAAQJANqtw83ma7qQRoc9sucgp
uUAhSd/JqDz7tnllrQHQdcyLMRSCBxvZ/i72YVixRRTHb1GVZ79iJWBmzh8ATLvj
uQIhAOuYWu6Vkve+zQ4Cd5EGWpytY/Or/6ZXvQf3L9ELIB07AiEAwI+miVT8t22w
Ge1IX+Q3L7lK2uBm97Pkwix9Wf7K2j8CIFUrQtQ1ZmgBpgeGhMr8zQ0O8a9JYqYz
2bZjefnMV9O5AiEAqSrKLKYcKm1To0NhLNUKYoPPLkCsVPqWgruhGDoOLfMCIE1E
kpJF13Dtq3KQOsaCoXbL4vo350vkBUrSovu45/6p
-----END RSA PRIVATE KEY-----

privately encrypted msgDigest:
64 bytes:
 8a c6 56 19 97 f5 e7 16 20 30 f2 2f 0e af 7c 28
 df 9d cd 5a 0e b0 11 c1 cc bb f2 3b 03 87 f0 96
 0d ce b4 55 dc 69 81 bc 30 40 75 9d 74 b8 b7 bd
 3b 15 a0 5d c2 db ab 9a 8d d3 f2 4b 77 e1 e9 a1

##############################################################

which matches the output from the command-line openssl.

Thanks for reading. If anyone can explain some of the anomalies noted, let us know.

Jerry


[1] The reason I used PKCS padding (-pkcs) is because if I change it to -oaep in the command-line test, I get an error message:
RSA operation error
 error:04066076:rsa routines:RSA_EAY_PRIVATE_ENCRYPT:unknown padding
type:rsa_eay.c:360:
which does not make sense because my version is:

Jerrys-Mac-Mini:Keys jk$ openssl
OpenSSL> version
OpenSSL 0.9.7l 28 Sep 2006

and "RSA_padding_add_PKCS1_OAEP() and RSA_padding_check_PKCS1_OAEP() were added in OpenSSL 0.9.2b" according to documentation:
http://openssl.org/docs/crypto/RSA_padding_add_PKCS1_type_1.html#

[2]
sub showHex {
  my $data = shift ;
  use bytes ;
  my $len = length($data) ;
  my $i ;
  my $show = "" ;
  for ($i=0; $i<$len; $i++) {
      my $value = ord(substr($data, $i, 1)) ;
      $show .= " " ;
      $show .= sprintf("%02x", $value) ;
      if ((($i+1) % 16) == 0) {
          $show .= "\n" ;
      }
  }

  return "$len bytes:\n$show" ;
}
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