I have been working on this guide during the install of my ProEFI and now that I've confirmed that everything is working ok I've decided to post it here. DaveT has posted a great install guide over in the SP section. We did a few things a bit differently so I figured I might as well put mine out there as well in case it helps someone.
----------------------------------------------
The following guide is how I connected my ProEFI 128 system into my 1995 6-Speed. I cannot confirm that the wire colors and connectors are the same for obd2 Supras.
Installation tips:
I perfer to solder and heat shrink all connections
The pins for additional wires to the ProEFI harness can be crimped with pliers and then soldered
Instructions for connecting the iBoost knob, CAN display cable, and wideband sensor are included with the ProEFI so I did not cover them here.
Items that can be removed:
Here is a list of some of the items that can be safely removed when the ProEFI is installed with a single turbo and upgraded fuel system.
All of the VSV’s that controlled the stock turbo system
The pressure tank and its VSV
The EGR vsv (if you have also removed the EGR system and have block off plates)
The stock FPR and FPR VSV
The TRAC ECU
The fuel pump ECU
The stock turbo pressure sensor
Traction control:
For the traction control connections to the wheel speed sensrs must be made.
Driven Wheel Speed Input (J1 A01)
Non-Driven Wheel Speed Input (J1 A12)
Wheel Speed Return (J1 A32)
The wheel speed sensor wires can be accessed at the ABS ECU which is behind the radio. After removing the dash panels and radio, locate the ABS ECU.
You need to get to the two left plugs shown unplugged here:
Unplug all three connectors and pull back the carpet on the drivers side to allow you to pull the harness out the side of the center console. You need to make connections to the White wire (Front LH sensor wire Pin 5) on the large connector and the purple wire (Rear LH sensor wire Pin 9) on the smaller connector and the light green wire (Return pin 1) smaller connector.
reconnect the three connectors to the ABS ECU and run the two tapped wires to the ProEFI harness.
Connect the shield ground to a good ground near the ABS ECU. You can see I connected the shield to the bolt on the left in this picture.
Connect the wire connected to the white wire to (J1 A12), the wire connected to the purple wire to (J1 A01). Splice the wire connected to the light green wire (return) to (J1 A32). Note that for some reason my harness came with these two line already connected to the ECU harness as if I had an automatic transmission. Just remove the wires from the ProEFI connector and insert the two wires from the speed sensors.
Trac Switch Input (J1 C11)
Trac Active Light Output (J2 B21)
Trac Enabled Output (J2 B02)
The TRAC Switch, the “TRAC OFF” light, and the “TRAC” light, and can all be wired to the connector that went to the stock TRAC ecu right next to the main ECU. There is a 26-pin connector here. Connect (J1 C11) to the light green wire, pin 5. Connect (J2 B21) to the White wire pin 24. Connect (J2 B02) to the light green/red stripe wire, pin 23.
Below is the connector from the TRAC ECU.
Here are the three wires I connected to:
Note, you must also cut the light green/red wire at the ABS/TRAC relay box on the passenger side of the engine bay. I do not have a picture of this. If this wire is not cut, the "TRAC OFF" light will be forced on all the time.
----------------------------------------------
The following guide is how I connected my ProEFI 128 system into my 1995 6-Speed. I cannot confirm that the wire colors and connectors are the same for obd2 Supras.
Installation tips:
I perfer to solder and heat shrink all connections
The pins for additional wires to the ProEFI harness can be crimped with pliers and then soldered
Instructions for connecting the iBoost knob, CAN display cable, and wideband sensor are included with the ProEFI so I did not cover them here.
Items that can be removed:
Here is a list of some of the items that can be safely removed when the ProEFI is installed with a single turbo and upgraded fuel system.
All of the VSV’s that controlled the stock turbo system
The pressure tank and its VSV
The EGR vsv (if you have also removed the EGR system and have block off plates)
The stock FPR and FPR VSV
The TRAC ECU
The fuel pump ECU
The stock turbo pressure sensor
Traction control:
For the traction control connections to the wheel speed sensrs must be made.
Driven Wheel Speed Input (J1 A01)
Non-Driven Wheel Speed Input (J1 A12)
Wheel Speed Return (J1 A32)
The wheel speed sensor wires can be accessed at the ABS ECU which is behind the radio. After removing the dash panels and radio, locate the ABS ECU.

You need to get to the two left plugs shown unplugged here:

Unplug all three connectors and pull back the carpet on the drivers side to allow you to pull the harness out the side of the center console. You need to make connections to the White wire (Front LH sensor wire Pin 5) on the large connector and the purple wire (Rear LH sensor wire Pin 9) on the smaller connector and the light green wire (Return pin 1) smaller connector.

reconnect the three connectors to the ABS ECU and run the two tapped wires to the ProEFI harness.
Connect the shield ground to a good ground near the ABS ECU. You can see I connected the shield to the bolt on the left in this picture.

Connect the wire connected to the white wire to (J1 A12), the wire connected to the purple wire to (J1 A01). Splice the wire connected to the light green wire (return) to (J1 A32). Note that for some reason my harness came with these two line already connected to the ECU harness as if I had an automatic transmission. Just remove the wires from the ProEFI connector and insert the two wires from the speed sensors.

Trac Switch Input (J1 C11)
Trac Active Light Output (J2 B21)
Trac Enabled Output (J2 B02)
The TRAC Switch, the “TRAC OFF” light, and the “TRAC” light, and can all be wired to the connector that went to the stock TRAC ecu right next to the main ECU. There is a 26-pin connector here. Connect (J1 C11) to the light green wire, pin 5. Connect (J2 B21) to the White wire pin 24. Connect (J2 B02) to the light green/red stripe wire, pin 23.
Below is the connector from the TRAC ECU.

Here are the three wires I connected to:

Note, you must also cut the light green/red wire at the ABS/TRAC relay box on the passenger side of the engine bay. I do not have a picture of this. If this wire is not cut, the "TRAC OFF" light will be forced on all the time.