I use MS1 V2.2 and yes with the TFi module. Firmware version I don't remember right now, but it was the latest firmware when I bought the unit and this was March 2012.

Can't quite help you with that really, in my case everything was just followed from these instructions and the car fired right up and has been doing so since.

-EDIT- I believe my firmware is 029y4a, which has been the latest version for quite a while now. Can't check it now tho, since I have removed the ECU from this car for winter time.
But I don't know if this relates to you at all, since you have MS2 and I have MS1.