So I powered up the unit and was able to load the firmware. I went to open a base map that I downloaded from the DIYPNP site in tunerstudio and it told me that it had a different signature (MS2E 2.1.1a vs my MS2E 3.0.3s). I loaded it anyways. Then it asked me if I wanted to send and burn it to the controller. I said ok. It said that there were a few errors, I reviewed the log and there were 5 warnings saying that certain values were ignored because they aren't in the current configuration.
Is that something I should expect since the file signatures were different?