Looking at the schematic (http://ftp1.digi.com/support/documentation/3001120101_b.pdf), it would appear that you should use the RCM3209 or RCM3229, which include the necessary resisters for "external serial port B".
But switching to those models would remove the NAND flash, status LEDs and reduce data RAM from 512KB to 256KB.
If this is a low-volume product, you could try populating R72, R82, and R83. Keeping PD1 high should disable the SD Card socket.
Alternately, you could use the SERB_USEPORTD macro to move serial port B from PC4/PC5 to PD4/PD5 and update your design accordingly.