looks like it lost communication with the TCM (Transmission Control Module) which will keep the programming from taking hold.
Did your Jeep go into limp mode at any time?
What else has changed?
Try this to reset the ECU:
1. Disconnect the battery by removing both battery cables.
2. Touch positive cable to the negative cable for 30 seconds to erase the electric charge in the capacitors. Do not allow them to touch the battery posts.
3. Reconnect the battery.
4. Turn the key to on but do not start.
5. Turn the headlights on.
6. Turn the headlights off.
7. Turn the key off.
The ECU has now been reset to its factory settings. For the next 50 warm-up periods the ECU will re-learn the engine and driving habits for your driving conditions and the newly installed parts.
Plug in your ODB and clear all codes.
Turn off and on for a couple of cycles - do not drive the Jeep.
Check for codes and try to program your changes.