There is a way to force a 003 or 003 Rack into a "Load Firmware" mode, then you can launch Pro Tools and it will prompt you for the firmware update.

Try this with an under 12 foot FireWire cable.

To force this mode (same on 003 and 003R):

With the unit off hold down 'Aux In->7/8' and the 'Mute' button (next to the Monitor knob), and then turn on the power to the unit. On 003 you'll see the display say "Load Firmware" and the MIDI Lights (In, Out1, Out2) will all start flashing. The MIDI lights flashing is the only indication on the 003 Rack that the unit is in this mode.

Once it is in this mode, launch Pro Tools, and you will see the message, "003 has firmware version x.xx, do you want to update..." Click the Update button to upload the 003 firmware.