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OK, This would mean the vehicle is in theft mode. There is only one thing you can try and it may or may not work. Here you go: (Make sure keys are not on same key chain)
It is not normal for the code reader to not be able to read the PCM, But it will not allow you to not start the car, It will just give you no communication.
The fuel pressre will drop to zero with key off.
The wires between the PATS Module and the PCM should not have come disconnected and if they did, This may be your cause of the vehicle in theft mode.
Another way to see if vehicle is in theft mode, If you have no spark while cranking, Then the vehicle is most likely again, In theft mode. PATS shuts off spark
The code reader not being able to scan with the car should have nothing to do with the car starting like I said before, It was a little confusing. Eventhough it is possible but is a not usual and not usual that the PCM needs reprograming. Usually when you cannot communicate, It is just a blown fuse for the cig.lighter/dlc connector.
When the theft light blinks fast when trying to start the car, Which is what you are saying to me, The car is in theft mode. I do strongly believe the next step is to program the keys. If the PCM was bad, the light would be steady when trying to start which indicates the PATS system is working correctly.
It is fuse 23 on the inside of the car, That is the battery Junction Block, You want the central junction block in the drivers side kick panel