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Hi, My name is Jay
Is your vehicle the 5.0 Mustang GT? If so the first code Po1289 is for the cylinder head temperature sensor. Check to make sure it is connected and not damaged? The second code is for the computer has not learned the camshaft timing pulse wheel. This can be due to damaged sensor or damaged cranks shaft sensor or if you put in a PCM program change it can cause it.
Check to make sure camshaft and crank sensors was not damaged and go from there. You may need to have a factory scanner hooked up to relearn camshaft sensor wheel spacing.
It is on the back side of the passenger side head. Hear is a diagram showing location item 12.
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Ok. Since the computer was reprogrammed it may just need the cam relearn procedure done.