First Thang, as your question is nothing to do with the subject of this thread, (Alternators), you should really have started a new thread for your problem!! But we are where we are so:

It seems to me that these are a strange combination of codes. They mean the following individual faults:

P0122 - Throttle Position Sensor circuit 1 low voltage

P0182 - Engine Fuel Temp Sensor circuit low voltage (high temperature)

P0193 - IP Sensor sensor circuit high voltage (high pressure)

P0222 - Throttle Position Sensor circuit 2 low voltage

P1108 - Manifold Absolute Pressure Sensor circuit high voltage

P1532 - Inlet Manifold Tuning valve 2 (bottom) circuit malfunction

P1549 - Inlet Manifold Tuning valve 1 (top) circuit malfunction

P1603 - Transmission Control Module EEPROM failure

That last fault - the EEPROM failure - suggests a possible cause of the whole situation; when doing all that work on your car, do you recall if you disconnected the battery while the ignition was switched ON? If you did, that unfortunately could do all sorts of damage to various modules. Because the codes suggest all sorts of voltage supply problems to many engine sensors, it does seem possible that you have a faulty ECU and TCM.