I typed "security export-smartcard" in the terminal. Indeed, it knows the Smart Card is there and correctly displayed the certificates, private keys, and identities on the card. I'm using a SCR3500 reader on a new MacBook Pro in this case. I get the same result with SCR3311 on an iMac too.
Something is still amiss, as I can't get Pulse Secure to connect to our protected network via VPN. In El Capitan, installing Smart Card Services (or Centrify) was a prerequisite to getting Pulse Secure working.
I wouldn't know where to begin in manually extracting the relevant pieces from the OS 10.11 installer and putting them on my machine. Is there a description of what to do somewhere?
Brian