I can't say much on the air fuel controller issue. Although when a did a quick google search on code P1121. It came up with this "TP Sensor Inconsistent With MAF Sensor". I didn't find anything regarding the air fuel controller. So your TPS could be faulty?
If you want to learn more on your SCT, I am pretty sure there is lots of info over on the SCT website.
I have read before that the older TKO's have some problems with high rpm shifts, which doesn't jive well with the cobras 6800rpm rev limit. That or the 2nd gear synchro is worn.