I reviewed the post and in the final post details the below:
- The card reader is now properly updated and functional with El Capitan
- When the card is inserted, the lights flash and the card is read into the Keychain.
- The card shows up in the Keychain with an expected prefix and Keychain name
- The certificates on the card all show up and are correctly detected
- The certificates are also all trusted through the chain
- The SystemCACerts keychain is also imported and up to date.
All the above items are good for me however I still get the same, cannot open message in Safari and Chrome.