2001 3.8L Windstar Intake Manifold Swap - NEED HELP!!

Hello Everyone, I'd like to start off saying that I'm new to this and not very mechanically inclined so please bear with me.

I have a 2001 3.8L V6 Manual(Stock Transmission) that I bought with the following already installed: Split Port Intake Manifold swap from the Windstar Van, also has unknown brand Long Tube Headers, unknown brand CAI, and 65mm Throttle body. Also an apparent 4.2L Camshaft Swap but I'm unsure of that because without tearing it apart there is no way to confirm or deny.

So, the Check Engine Light is on with these codes on Global OBD2; P0412 Secondary Air Injection Switching Valve A Circuit, P0118 Engine Coolant Temperature Sensor Signal Circuit is Open.

It also has these codes listed under Ford OEM Enhanced; P1401 Differential Pressure Feedback EGR Circuit High Input, P1409 EGR Vacuum Regulator Solenoid Circuit, P1131 Lack of HO2S11 Switches - Sensor Indicates Lean, P1127 Exhaust Temperature Out of Range, O2 Sensor Tests Not Completed, P1124 Throttle Position Sensor A Out Of Self Test Range, and P1101 Mass Air Flow Sensor Out Of Self Test Range.

I figured the two EGR codes are coming from the Manifold Swap, and the Exhaust Temperature is from the Long Tube Headers.

My overall question is, Do I have a genuine issue with the motor, is it just a small part/hose that I need to add to have this intake manifold swap done properly, OR has it been done properly and just now needs tuned for the computer to properly recognize what's happening?
 
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Do you have an ODB2 scanner?

If not, do you:
  • Have a Volt-Ohm meter (VOM)
  • A test light.
  • A set of wiring diagrams (you may need these anyway).
  • A good working knowledge of how to trouble shoot electronic sensors on a modern car?
  • Lots of patience
Here's some information on an affordable Windows based scanner.

ForScan ODB2 scanner w ELM327 USB
https://www.stangnet.com/mustang-forums/resources/forscan-odb2-scanner-w-elm327-usb.57/

IF this were my car I would start with a simple circuit and verify the 5 volt reference and then the signal returns while watching the value as displayed on the ODB2 scanner.

P0118 Engine Coolant Temperature Sensor Signal Circuit is Open.
For the 5 volt reference this should be GY/RD wire. IF by chance the 5 volt reference line is missing this could explain why most (or all) of the sensors are having problems.

With the amount of work done on this car I would also confirm that the motor grounding strap is in place from the left hand motor mount to the frame rail.
 
Like I said in the beginning please bear with me as I'm new to all of this, I may overlook some things.

I was checking under the hood, trying to compare it to my daily driver that still has the original intake manifold, these 3 plugs are just hanging there loosely, and this is what they are normally plugged into. I'm unsure what the gray oval shaped one plugs into I can't find it on my daily? unless its something transmission related my daily is auto the modded one is manual.

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In the second picture the part you are pointing at is a vacuum solenoid for the EGR. This is apparently not a Calif. car since it doesn't have the vacuum solenoid for the air pump. The vacuum diagram on the underside of the hood should show you what parts are supposed to be present. If connectors are not hooked up it's not surprising you are getting codes.
 
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In the second picture the part you are pointing at is a vacuum solenoid for the EGR. This is apparently not a Calif. car since it doesn't have the vacuum solenoid for the air pump. The vacuum diagram on the underside of the hood should show you what parts are supposed to be present. If connectors are not hooked up it's not surprising you are getting codes.

No I'm in good ol' West Virginia lol, so for those codes what would I need to do? Tune it out? Buy a delete part to plug into it? or Figure out how to reinstall an EGR?
 
P0412 has to do with the air injection. I thought this was only present on the Calif. cars. If the original exhaust manifolds were replaced with headers there would no longer be the connections for air injection.

As to what to do about the codes, it depends on whether you need to have smog inspections in your state. If you don't need smog inspections the car could still be driven as is, with the understanding that it is a violation of federal law to remove smog equipment. If you need smog inspections the best option is probably to switch back to the original parts.