Toyota IGT is typically a 5V signal, 0v 5V transition begins charging the coil then spark occurs when it transitions from 5v to 0v.
I am not 100% sure the IGT on the 1gge ecu is 5v, but if it is 5V, it would almost be impossible that if that IGT output had failed it would default to 12v.
Is there another 5V output pin on the ecu you can test to confirm its 5V out?
Have you attached all the grounds to the ecu? There may be a pull down resistor that's floating at 12v if the ground isn't connected, but seems unlikely.
Have you double checked you have the right pin for IGT and confirmed the pinout you are using is the correct one for your ecu? Are you able to post up the pinout/wiring diagrams you do have?