I'm just using an sct from bama. I called them up and talked it over with them and they swear there is no such adjustment, they also say the ECM doesn't care what the transmission ratios are. I ended up getting the 'we'll look into it and get back to you' line and haven't heard anything since.
Umm..the trans ratios absolutely can and need to be adjusted in the tune. Just another reason why I think bama tunes are dangerous. If they told you that..just..wow..
If it is misfire codes then you need to do a neutral profile relearn with an IDS.
^ this