HID multiCLASS RFID reader all Mifare to Wiegand 32bit
For this specific reader, communication is only one way, from the reader to the Arduino via Weigand protocol.  Because of this, changes to the configuration for these readers is handled by proprietary RFID cards obtained from HID Global. The reader reads the card, and changes its configuration accordingly.  I was able to reach out to HID Global technical support and they are sending me a card that will change the configuration to output 56bit CSN/CSR/UID for mifare cards (which will cover the 7byte UID of mifare ultra).

Thanks for the comments that helped me work this through.