As a total noob, let me see if I understood the basic steps. Particularly, do I need to set the baud rate in the command line. And I should probably make a backup (read) before flashing the chip.

Prerequisite. DC power supply with minimum 13.5 V or if you have to flash in the car be sure to connect a batter charger.

1. The Immo3-chip (95040) should be in Boot Mode before reprogramming
This is achieved by "touching PIN 24 on the flash chip (800BB) to ground before turning on your switch/ignition signal. Turn on the ignition switch and remove the ground from PIN 24 about 2-3 seconds later. You are now in BOOT MODE."
http://www.nefariousmotorsports.com/wiki/index.php/ECU_Boot_Mode

2. Buy/loan a Galletto cable
Dumb k-line cable via the OBD-II interface is OK to read the chip. BUT, in order to reprogram the chip in Boot Mode, you need to get a suitable cable (clone), such as Galletto 1260.

3. Use the "ME7_95040" command tool sw to access the chip
Sw + manual can be downloaded here:
http://nefariousmotorsports.com/forum/index.php?topic=1168.0

4. Use a sw pack to overwrite the code in the 95040-chip and set Immo3 to OFF
The necessary predefined bin-files (e.g. Immo off.bin, or immodef95040) can be downloaded from here:
http://nefariousmotorsports.com/forum/index.php?topic=2973.0title=

5. Execute the command and wait 2-3 minutes
Command file and bin file must be in same directory. Open the cmd.exe window in Windows and run:
c:\me7_95040 --bootmode -w -p 3 immodef95040