Need help . Electrical issue

Ok so I have a 2002 3.8 v6 .I recently did a engine replacement on it. Car will run but won't stay running. I had it diagnosed. I have 13 codes. I will tell u what I have changed and replaced.
1. Spark plug wires
2. Crank and cam sensor
3. Main engine wire harness.
4. I cleaned the injectors and replaced the rail
5.new o2 sensors and maf sensor, i.a.c
6. New fuel pressure sensor
7. New fuel filter.
Now the car is running rich .I checked the plugs today and they are black. The codes I am throwing are . P1124,p1780,p0703,p1408,p1137,p0113,p0102,p0193,p1519. Some of the codes coming up aren't even engine related ones a od switch and other is brake switch which is brand new. I'm so confused as to what I can do . This is my daily driver for work it's been down now for almost two months. I need it running. I looked into all the codes. I am a mechanic . But this car is testing me. Sorry for long post. Any help will be awesome. Thank you for your time .
 
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Note. I'm a big believer in Occam's Razor. Occam's Razor says that it's likely there is a common cause to all of the DTC codes.

If this were my car the first thing I would look for is damage to the wiring harness. Not finding anything I would be thinking there's a problem in the car's 5 volt VPWR reference circuit. For example:
  • open in VPWR ground
  • VPWR shorted to a 12 volt circuit
  • bad sensor pulling down VPWR
If this were my car I would verify the power and ground at each sensor called out to see IF the correct voltages are present. Use a test light that will "load" the circuit. Especially the +12 volt circuits.

P1124 - Throttle Position (TP) Sensor Out of Self-Test Range
P1780 - Transmission Control Switch Out of Self-Test Range
P0703 - Brake Switch Circuit Input Malfunction
P1408 - EGR Flow Out of Self-Test Range (Non MIL)
P1137 - Lack of HO2S-12 Switch, Sensor Indicates Lean
P0113 - Intake Air Temperature (IAT) Circuit High Input
P0102 - Mass Air Flow (MAF) Circuit Low Input
P0193 - Fuel Rail Pressure Sensor Circuit High Input (FRP)
P1519 - Inlet Manifold Runner Control Malfunction (Stuck Closed)
 
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Note. I'm a big believer in Occam's Razor. Occam's Razor says that it's likely there is a common cause to all of the DTC codes.

If this were my car the first thing I would look for is damage to the wiring harness. Not finding anything I would be thinking there's a problem in the car's 5 volt VPWR reference circuit. For example:
  • open in VPWR ground
  • VPWR shorted to a 12 volt circuit
  • bad sensor pulling down VPWR
If this were my car I would verify the power and ground at each sensor called out to see IF the correct voltages are present. Use a test light that will "load" the circuit. Especially the +12 volt circuits.

P1124 - Throttle Position (TP) Sensor Out of Self-Test Range
P1780 - Transmission Control Switch Out of Self-Test Range
P0703 - Brake Switch Circuit Input Malfunction
P1408 - EGR Flow Out of Self-Test Range (Non MIL)
P1137 - Lack of HO2S-12 Switch, Sensor Indicates Lean
P0113 - Intake Air Temperature (IAT) Circuit High Input
P0102 - Mass Air Flow (MAF) Circuit Low Input
P0193 - Fuel Rail Pressure Sensor Circuit High Input (FRP)
P1519 - Inlet Manifold Runner Control Malfunction (Stuck Closed)
Thank you for responding. I have found the issue with my car. I had a broken throttle body . The whole bottom of it was cracked and litterally fell in my hands when I undid the top too bolts. So I swapped them out car runs perfect . No more codes