This might sound crazy but did/do you have autostart on your car ?
Before I swapped to manual I had auto start from viper. after the swap the card would not start and we tried a bunch of stuff.
There's a key inside a small box that connects to the alarm and the started and that's how the auto start would start the car since it needed to detect a key in the ignition. The key I had after the swap belonged to the J30 ecu and I had since swapped to the J32. After removing the key and placing one from the current ecu the car started right up.
Hope you get resolution fast.