Subaru's are picky when it comes to scan tools. I doubt the ECU or TCU is the problem as it is pulling codes okay. More like that scan tool just does not like that car. Happens all the time, one of the reasons why it costs a ton to operate a shop, you need to have four or five tools to talk to everything.
That said, yes installing a spare will put the transmission into limp mode if it is any different in diameter than the other three tires on the car. Next, to get it out of limp mode should simply take replacing the spare with the correct sized tire. However, the flashing temperature light will keep it in limp mode as well. For that you need to use a meter to test the sensor as well as verify that the transmission connector is clean and secure. As the transmission was out it could be a loose or corroded connection or just a bad temperature sensor.
My first thing would be to have a different scan tool attached and see what that shows first. Then see if the sensor is showing an odd reading, like 200 degrees when the car was just started and cold or -40 when it is warmed up. Then go from there.
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Wednesday, April 11th, 2018 AT 1:12 AM