Ok, so previously, I have flashed a lot of different tunes onto cars and had no immobilizer issues. The last ME9 I did, I had the immo shut down on me. We got the vehicle going again by installing a new ECM, adapting it, then adapting a new (used) cluster, and then once it ran we went back to the old cluster, and all is fine with that. The original ECM is so far not useable, I cannot get my Galletto to connect to it (or the working ECM actuallyl so something is just up there.

My problem is that for whatever reason I can't get a read on this ECM either. It says security code not ready, which I've heard with the Kess V2 box could just be a matter of me needing to leave it on for a long time until it stops saying that. Thats reallly a question for them at Alien Tech.

Regardless, I should be able to just make a tune on the stock file that I've downloaded from Nefmoto and upload that, correct?

If you have a backup; BDM it...
Otherwise BDM another core with IMMOB defeat

you need mpps v16 or bdm , then edit the eprom