Thanks for the password.
There is a 7 pin connector for the Emergency stop in and out. It has a mate with a jumper wire attached to the Topaz end. If you put the jumpered mating connector on this, the emergency stop errors go away.
The other connector is a 12 pin connector. There is no mating connector on the Topaz for this connector. The HDLC data comes out on this connector. When this connector is not connected to the LCS, the Topaz cannot program the Head I/O board or the Conveyor I/O board. There is either a loop back in the LCS, or differential signal termination to make the serial HDLC buss work.