I'm in the same boat man. Building the circuits and tuning the car is no issue but I haven't played with any coding and .ini manipulation on these controllers. Arduinos, matlab, labview, sure, but not this stuff.
I was thinking it'd be cool to have a MAC boost control solenoid drop boost if the coolant pressure sensor saw a 5%+ rise in coolant pressure but those aren't default options so it'd require some custom settings to be created. I'm sure some guys in the megasquirt facebook groups could teach us how that part is done. That is if I don't end up switching to MS3X or Pro beforehand.
I can't open these files at work but can you send a picture of the wiring? Are you sure you're using the right pins on the "options" connector? I had one guy counting the pins backward so his wideband was pinned in the wrong location. Also make sure this is the newer version with the 26 pin rather than the old 15 pin version.