how are you going about writing to this ECU? Is it only able thru boot mode and those Master/Slave tuning boxes?
Nope, I just use the Nefmoto software and an ebay cable. The trick is, that you need to pull the ECU out, read the 95040 coding, disable the immo and then you can flash to your heart's content.
Best bet is to buy a spare ECU, make a bench flasher and do all your flashing that way. At that point, you can always swap between the two and do your file revisions that way.
What I did was bought a plug in voltage adapter that puts out between 13.5-15v, then I plug in a power inverter to my cigarette lighter in my car. From there, I can log on the road, pull over with my laptop, make changes, plug in the voltage source to the inverter and hook up my bench flasher, flash the spare ECU while I'm on the side of the road and swap them out (takes all of 3-4 minutes). I've literally done hundreds of file revisions that way.