Ford 99-04 Mustang – AMP-PNP-NE9904 – Installation

Jump to: Installation | Software | I/O Configuration | Jumper Matrix | Rear Options Connector


ECU Model / Vehicle Specific Installation Guide

Vehicle Fitment:

  • 1999-2004 Ford Mustang SOHC V8 - Manual Transmission

Please read all documentation before installing your AMP Plug-N-Play ECU and verify that you’ve followed all steps before starting your engine for the first time.

Physical Installation

All you’ll need for a successful installation are some basic hand tools. No cutting or drilling of the original sheet metal or bracketry is required.

For a thorough and professional installation, you will need the following items:

  • Ratchet
  • 5.5mm Socket
  • 7mm Socket
  • 8mm Socket
  • Trim Pin Removal Tool
  • Zip Ties
  • Laptop
  1. Disconnect the negative battery cable
  2. Factory ECU Location - Passenger Footwell
    The stock ECU is located in the passenger-side footwell, just behind the kick panel that is located in front of the passenger door.
  3. Remove the Door Sill
    Begin by removing the passenger side door sill by lifting upward from the rocker at the front and working toward the back of the car
  4. Remove the Passenger Kick Panel
    Using a Trim Removal Tool, remove the kick panel push-pin in the bottom-left corner of the panel. Optionally, remove the door sill to make easier removal of the kick panel.  Then, gently pull on the kick panel that is held by two push-pins.
  5. Disconnect the A & B Body Harness Connectors
    There are (3) body harness connectors located in front of the main ECU harness. Disconnect Connectors A &B by pressing the retention clip and pulling upward on the top half of the connector. Pull on the connector body and not the wires.
  6. Disconnect the C Body Harness Connector
    Disconnect Connector C by using a pick and gently pulling away the retention clip on each side of the connector while pulling upward on the top half of the connector. Pull on the connector body and not the wires. These clips are fragile, so use extreme care.            
  7. Remove Ground Screw
    Using an 8mm socket, remove the green ground screw under Connector C
  8. Remove Body Harness Connector Bracket
    Using a 7mm socket, remove the two screws that secure the connector bracket
  9. Disconnect the Main ECU Connector & Remove Factory ECU
    The ECU harness is held in the ECU by the large bolt in the center of the connector.  Using a 10mm Socket & Ratchet loosen the bolt in the center of the harness until the harness comes out of the ECU. The bolt will remain in the ECU connector and will not come out completely.  Finally, Remove the 5.5mm mounting screw securing the factory plastic ECU bracket. Then slide the ECU free from the bracket.
  10. Route the Vacuum Line through the firewall
    Option A: The vacuum hose can be passed through a grommet in the firewall through which the air conditioning lines pass. From the engine bay side of the fire wall on the passenger side, work a couple inches of hose through the lower right corner of the grommet. Be sure the vacuum line is routed without kinks or pinching.
    Option B: Pull back the gasket flap next to the evaporator drain line and drill a 1/4″ hole immediately to the right of the drain line from within the footwell.  Install the supplied barbed bulkhead fitting into the hole. Optionally, seal the firewall with RTV.
  11. Remove Factory Vacuum Coupler
    On the passenger side of the engine bay against the firewall, locate the white OEM vacuum hose junction as seen in the following image. Separate the two vacuum lines at the junction by twisting/pulling and remove the coupling tube in the middle.
  12. Install Supplied Vacuum Line Tee
    Insert the supplied vacuum tee as shown and attached the vacuum line.  

  13. Wiring the Rear Options Connector

    This is the time to wire in your wideband along with completing any optional wiring you plan to use through the Rear Options Connector. This is the best time to wire additional sensors, inputs, outputs, speed inputs, or ignition upgrades, since the connector is easier to access before the ECU is mounted in the vehicle.

    Internal Wideband ECU Models
    If you selected the Internal Wideband ECU model, connect the provided wideband sensor cable to the rear options connector as instructed in the pinout section. This allows the wideband sensor to plug directly into the ECU without using a separate external wideband controller.

    No Wideband ECU Models / External Wideband Setups
    If you selected the No Wideband ECU model, or if you are using an external wideband controller, wire the external wideband controller signal to the appropriate rear options connector input.  Click Here: Wiring a Wideband Controller

    Additional Inputs and Outputs
    We also recommend wiring any other planned sensors or accessories at this time, including additional analog inputs, digital inputs, speed inputs, or outputs. This helps avoid removing or accessing the ECU later as your setup expands. Once your wiring is complete, plug the rear options connector into the ECU until it clicks into place and neatly secure the wiring. Refer to the Rear Options Connector section for pinout details and available functions.

  14. Connect the supplied Tuning Cable
    Attach the provided tuning cable to the ECU and tighten the collar clockwise until snug with your fingers. Be sure the pins are aligned properly before tightening.
  15. Install the AMP Play-N-Play ECU
    Installation is the reverse of removal. Slide the ECU in the factory location and secure it using the original plastic ECU bracket and screw. Please note that the bracket fitment will be slightly tighter due to the vacuum nipple next to the connector. 
  16. Connect the Vacuum Line to the ECU
    After the ECU is mounted, connect the vacuum line the was done on Steps 5/6 to the vacuum port on the ECU. The vacuum port nipple is located on the right-side of the ECU.
  17. Reconnect the Main Harness
    Reconnect the main harness to the ECU using the 10mm socket.  Tighten until the connector is fully seated into the ECU.
  18. Reinstall the Ground Screw
    Reinstall the ground wire and ground screw. It is advised to remove any rust or corrosion that may have developed on the contacting surfaces of the ground area before assembling.  While tightening with an 8mm socket, ensure the ring terminal’s locking tap is properly engaged with the slot just below the screw hole in the car.
  19. Remove Body Harness Connector Bracket
    Reinstall the connector bracket and secure with the two screws previously removed. Tighten both screws with a 7mm socket.

  20. Reconnect the Body Harness Connectors
    Push the floor carpet back into place.  Reconnect the three wiring connectors ensuring that each securely clicks into place.
  21. Reinstall the Kick Panel and Door Sill
    Reinstall the foot well kick panel and secure into place with the previously removed retention pin.  Reinstall the door sill trim. Light tapping with a rubber mallet may be necessary to properly seat it.  Reconnect the Negative Battery Cable.
  22. Mass Air Flow Meter Removal
    The preloaded base tune on your AMP Plug-N-Play ECU is configured for Speed Density, which is how most customers choose to tune these applications. Because of this, the factory mass air flow meter is no longer required and can be removed from the vehicle. If you are not removing the MAF Sensor you must UNPLUG the sensor.

Software

Tuning Software Installation & Setup

Before starting the vehicle, install TunerStudio on your laptop and connect to your AMP Plug-N-Play ECU using the supplied tuning cable. Open TunerStudio, create a new project for the ECU. Once connected, confirm that TunerStudio shows the ECU as Online and that communication is working properly before making any changes.

View Tuning Software Installation & Setup Instructions 

Initial Configuration

Your AMP Plug-N-Play ECU includes a base tune that is configured for a stock application. If your vehicle has any changes from stock, you should review and update the tune BEFORE STARTING THE VEHICLE.

Examples of settings that may need to be reviewed or updated include:

  • Engine Size
  • Injector Size
  • Wideband Controller

Confirm that all required settings match the components installed on your vehicle before proceeding with startup and timing verification.

View Initial Configuration Instructions →

Tuning

Congratulations, you have completed the physical installation, software setup, and initial configuration of your new AMP Plug-N-Play ECU. Your ECU is now ready, and you can begin tuning the vehicle.

Base Tune

Your AMP Plug-N-Play ECU is preloaded with a base tune for the specific ECU model and vehicle application it was built for. This provides a proper starting point for initial startup and tuning. If you ever need to restore the original base tune to the ECU, you can download it from our Firmware & Base Tunes page.

I/O Configuration

Below is a breakdown of the I/O usage for your AMP Plug-N-Play ECU. This identifies the default pin assignments for your specific vehicle, allowing you to see which inputs and outputs are already being used for factory functions and why those pins may not be available for use in the tune.

ECU Internal Jumper Matrix

Below is a diagram and overview of the available internal jumpers and their functions. To access the jumpers, remove the (6) screws from the top cover of the ECU.

JP2: Transmission Control Pull-Up

This jumper is only used on applications that are equipped with the internal transmission controller.  When the jumper is applied it adds a pull-up to the Range Selector on the transmission.

Digital Range Selector - No pull-up

Analog Range Selector - Requires pull-up

Default Setting: Not Jumpered

JP4: AUX Vehicle Speed Input Sensor Type Select

The AUX Input Circuit is configured for a vehicle speed input which can use either a Hall Effect Sensor or a VR Sensor based on how the jumpers are installed on JP4.  In the tuning software (TunerStudio) this input is labeled Digital Frequency In 2.

Hall Effect Sensor: jumper Pins 1 & 2. This is factory configuration 

VR sensor: jumper Pins 1 & 3 and Pins 2 & 4

Default Setting: Pins 1 & 2 Jumpered

JP5: VSS Speed Input

This is configured for the factory Vehicle Speed Sensor (VSS) from the transmission. The VSS Speed Input Circuit is configured for a vehicle speed input which can use either a Hall Effect Sensor or a VR Sensor based on how the jumpers are installed on JP5.

Hall Effect Sensor: jumper Pins 1 & 2. This is factory configuration 

VR sensor: jumper Pins 1 & 3 and Pins 2 & 4

Default Setting: Pins 1 & 2 Jumpered

Switch: ECU/TCU

This switch is used to select which controller the serial communication from the M8 Tuning Cable is connected to. It should normally remain in the default ECU position. Only change the switch from ECU to TCU when you need to connect to the transmission controller, such as for a firmware update.

Default Setting: ECU

Rear Options Connector

Your ECU includes a bag containing (2) connector housings and (2) banded sets of pre-terminated wires. One set of wires is intended for the larger openings in the connector, and the other set is intended for the smaller openings. Reference the pinout below for available rear options connector functions and wiring locations.

Important: The pinout diagram below is shown from the back of the connector.

Printable Copy of Rear Options Connector