How to reset the wrench indicator?

What is your question?

I've had some issues with my Ford that require me to reset the KAM in PCM when it goes to a rough idle and stalls. By doing this reset the vehicle is usually good for a couple weeks and runs great. I disconnect the negative battery terminal run a jumper to the positive cable to drain the capacitors and then reattach the negative cable and let it go through the relearn process. (Idle for 10 minutes to get to operating temperature then turning on the ac for 5 mins, in gear for 5 mins with a/c off and on etc. Once I shut the vehicle off in the past the wrench and P2110 etc codes go away. However, this last time no matter what I do the wrench light will not go away and the car will not rev above idle. The throttle does work with the key in the on position watching the throttle body blades move they move freely when the pedal is depressed then released.. I did clean the TB but nothing seems to help. A little frustrated with this thing.

What makes this problem better or worse?