retrolefty:
Next time you want or need to send AT commands it's not nessesary to remove the atmega chip, just wire a jumper from reset pin to ground pin. That will isolate the chip but still allow the FTDI USB convertor chip to function.
This combined with swapping the RX/TX pins (rx -> rx & tx -> tx from the Arduino to the MdFly bt) worked perfectly to change my baud rate. This forum rocks. Thank you everyone!