Below is a list and ID info for the various connectors attached to the "Powertrain Control Module" harness...
Connections and modifications required to adapt this stock harness to it's new home are noted below.

Connector C-104 (female / black)
(42) terminals
Rectangular shape
Located in the RH rear of the Mustang's engine compartment above right valve cover.
Plugs directly into engine harness, no modifications required (wire details shown for referance only).
Pin 1 blank
Pin 2 Ckt101 grey/yellow
Pin 3 Ckt395 grey/orange
Pin 4 Ckt259 orange/red
Pin 5 blank
Pin 6 Ckt39 red/white
Pin 7 Ckt555 tan
Pin 8 Ckt556 white
Pin 9 Ckt361 red
Pin 10 blank
Pin 11 Ckt355 grey/white
Pin 12 Ckt351 brown/white
Pin 13 Ckt557 brown/yellow
Pin 14 Ckt558 brown/lt blue
Pin 15 Ckt559 tan/black
Pin 16 Ckt354 lt green/red
Pin 17 blank
Pin 18 Ckt359 grey/red
Pin 19 Ckt560 lt green/orange
Pin 20 Ckt561 tan/red
Pin 21 Ckt562 lt blue
Pin 22 Ckt258 white/pink
Pin 23 Ckt644 dk green
Pin 24 blank
Pin 25 Ckt94 red/black
Pin 26 blank
Pin 27 Ckt16 red/lt green
Pin 28 blank
Pin 29 Ckt570 black/white
Pin 30 Ckt352 brown/lt blue
Pin 31 Ckt31 white/red
Pin 32 Ckt687 grey/yellow
Pin 33 Ckt875 black/lt blue
Pin 34 Ckt11 tan/yellow
Pin 35 Ckt48 SHIELD
Pin 36 blank
Pin 37 Ckt74 grey/lt blue
Pin 38 blank
Pin 39 Ckt264 white/lt blue
Pin 40 blank
Pin 41 blank
Pin 42 blank

Connector C-106 (female / black)
(16) terminals
Square shape
Located near the Mustang's firewall, above the rear of the right valve cover.
Connects directly to the applicable 5.0 transmission/o2 sensor harness. No modifications required (wire details shown for referance only).
Pin 1 Ckt298 pink/orange
Pin 2 Ckt33 white/pink
Pin 3 Ckt32 red/lt blue
Pin 4 Ckt140 black/pink
Pin 5 Ckt199 lt blue/yellow
Pin 6 Ckt237 orange/yellow
Pin 7 blank
Pin 8 Ckt315 pink/orange
Pin 9 Ckt361 red
Pin 10 Ckt359 grey/red
Pin 11 Ckt923 orange/black
Pin 12 Ckt925 white/yellow
Pin 13 Ckt970 dk green/white
Pin 14 Ckt924 black/orange
Pin 15 Ckt679 grey/black
Pin 16 Ckt676 pink/orange

Connector C-108 (female / black)
(16) terminals
Located in front of the Mustang's passenger side strut tower, near the alternator.
Modifications/connections are required.
Pin 1 Ckt33 white/pink - connect to starter relay "S" terminal.
Pin 2 Ckt2 white/lt blue - no connection required (went to the Mustang RF turn lamp)
Pin 3 Ckt37 yellow - connect to battery thru a 20amp fuse.
Pin 4 blank
Pin 5 Ckt514 yellow/red - no connection required (went to Mustang ABS sensor).
Pin 6 Ckt516 yellow/black - no connection required (went to Mustang ABS sensor).
Pin 7 blank
Pin 8 blank
Pin 9 Ckt37 yellow - connect to battery thru a 20amp fuse.
Pin 10 Ckt57 black - connect to AC clutch field coil.
Pin 11 blank
Pin 12 blank
Pin 13 blank
Pin 14 Ckt347 black/yellow - connect to AC clutch field coil.
Pin 15 blank
Pin 16 blank

Connector C-109 (male / black)
(4) terminals
Located in front of the Mustang's passenger side strut tower, near the alternator.
Modifications/connections are required as noted below...
Ckt38 black/orange - connect to battery thru 60amp "FAN" fuse
Ckt570 black/white - connect to chassis and battery ground.

Connector C-115 (black) Ignition Control Module
(6) terminals
(6) wires attached.
Connector attaches directly to the module, mounted to the side of the Mustang's RH fender apron, forward of the strut tower.
No modifications required. (wire details shown for referance only)
Ckt11 tan/yellow
Ckt16 red/lt green
Ckt644 dk green
Ckt648 white/pink
Ckt875 black/lt blue
Ckt929pink

Connector C-117 - "SPOUT" (black)
(2) terminals
Located on RH side of the Mustang's engine compartment
Jumper plugs directly into connector.
No modifications required (wire details shown for referance only).
Ckt929 pink
Ckt929 pink

Connector C-119 (female / natural)
(4) terminals

Connector C-128 (female / black) AC High Pressure Cutout/Fan Switch
(4) terminals
Connector attaches directly to the switch, located in front of the Mustang's passenger's side strut tower.
No modifications required. (wire details shown for referance only
Ckt57 black
Ckt198 dk green/orange
Ckt420 dk blue/yellow
Ckt883 pink/lt blue

Connector C-135 (female / black)
(8) terminals
Located in front of the Mustang's passenger's side strut tower. Connects to MAF harness.
No modifications are required (wiring details shown for referance only)
Ckt359 grey/red (to IAT sensor)
Ckt362 red
Ckt743 grey (to IAT sensor)
Ckt967 lt blue/red
Ckt968 tan/lt blue
Ckt969 black
Ckt
Ckt

Connector C-145 (black)
(2) terminals
Located on right side of Mustang's engine compartment.
Connector plug went to the Mustang's right front ABS brake sensor, so no is connection required (wiring details shown for referance only)
These two wires only pass thru this harness, and come directly from connecor C-108.
Connector and wires can be removed if desired.
Ckt514 yellow/red
Ckt516 yellow/black

Connector C-165 (black) EGR Vacuum Regulator "EVR" Solenoid
(2) terminals
Connector attaches directly to the EGR vacuum regulator solenoid, located insidethe RH fender, above the tire splash panel in the Mustang.
No modifications required. (wire details shown for referance only)
Ckt360 brown/pink
Ckt361 red
ECA grounds ckt360 to energize solenoid.

Connector C-167 (grey) AC Clutch Cycling Switch
(2) terminals
Location in Mustang - RH rear corner of engine compartment, on AC accumulator.
Connector pluged directly onto the Mustang switch, but modifications are required as noted below.
Ckt348 pink
Ckt420 dk blue/yellow
The Ford switch was closed above 46psi, open below 23psi
These wires can be connected to your origional RX-7 pressure switch if needed.

Connector C-175 Secondary Air Injection Diverter "AIRD" Solenoid
(2) terminals
Connector attaches directly to the solenoid, formerly located inside the Mustang's passenger side front fender, above the tire splash panel.
No modifications required. (wire details shown for referance only)
Ckt200 brown
Ckt361 red

Connector C-176 (female) Secondary Air Injection Bypass (AIRB) Solenoid
(2) terminals
Located high on the inner splash panel on driver's side in front of the Mustang's passenger side strut tower.
Connector plugs directly onto the solenoid, so no modifications are required (wiring details shown for referance only)
Ckt190 white/orange
Ckt361 red

Connector C-192 (male) Constant Control Relay Module (CCRM)
(24) terminals (2 rows of 12)
Located above/behind the Mustang's radiator on the passenger side.
Connector plugs directly into the CCRM, so no modifications are required (wiring details shown for referance only)
Pin1 Ckt229 red/orange (cooling fan motor LOW output)
Pin2 Ckt229 red/orange (cooling fan motor LOW output)
Pin3 Ckt38 black/orange (BATT "+" cooling fan relay)
Pin4 Ckt38 black/orange (BATT "+" cooling fan relay)
Pin5 Ckt238 dk green/yellow (power to fuel pump)
Pin6 Ckt638 orange/lt blue (cooling fan motor HIGH output)
Pin7 Ckt638 orange/lt blue (cooling fan motor HIGH output)
Pin8 Ckt37 yellow (BATT "+" to PCM power relay)
Pin9 blank
Pin10 Ckt37 yellow (BATT "+" to PCM power relay)
Pin11 Ckt37 yellow (BATT "+" to fuel pump relay)
Pin12 Ckt361 red (PCM power)
Pin13 Ckt16 red/lt green (IGN- hot in "run"/"start")
Pin14 Ckt228 dk blue (low fan control input)
Pin15 Ckt570 black/white (ground)
Pin16 Ckt57 black (AC clutch coil ground)
Pin17 Ckt639 lt green/pink (high speed fan output)
Pin18 Ckt926 lt blue/orange (fuel pump relay input)
Pin19 blank
Pin20 blank
Pin21 Ckt198 dk green/orange (AC high pressure cutout/fan switch)
Pin22 Ckt331 pink/yellow (AC WOT cutout relay input)
Pin23 Ckt347 black/yellow (AC clutch coil control)
Pin24 Ckt361 red (PCM power)

Connector C-194 (female) Low Engine Coolant Switch
(3) terminals
Located on top of the Mustang's coolant recovery bottle.
Connector plugged directly into the low engine coolant switch, so no modifications are required (wiring details shown for referance only)
This circiut only passes thru this harness, so the connectors and wires can be eliminated if desired.
Ckt57 black (grounded in harness at G103)
Ckt640 red/yellow (goes to C-213)
Ckt794 lt blue (goes to C-213)

Connector C-198 (grey) Data Link Connector (DLC)
(1) terminal
Located near the firewall on driver's side in back of strut tower.
Connector plug is for diagnostic use only, so no modifications are required (wiring details shown for referance only)
Ckt209 white/pink

Connector C-199 (grey) Data Link Connector (DLC)
(16) terminals
Located in back of the Mustang's passenger's side strut tower.
Connector plug is for diagnostic use only, so no modifications are required (wiring details shown for referance only)
Pin1 Ckt915 pink/lt blue (data "-")
Pin2 Ckt359 grey/red (signal return)
Pin3 Ckt914 tan/orange (data "+")
Pin4 Ckt658 pink/lt green (self test output - MIL lamp)
Pin5 blank
Pin6 Ckt926 (2) lt blue/orange (fuel pump)

Connector C-213 (male)
(12) terminals (rectangular, 2 rows of 6)
Located behind the Mustang's instrument panel, under the cowl.
Modifications/connections are required as noted below...
Pin1 Ckt224 tan/white - was connected to the AODE's Transmission Control Switch Module (if equipped).
Pin2 blank
Pin3 Ckt794 lt blue
Pin4 Ckt640 red/yellow - not required, buy was connected to 10a fuse to power the Mustang's low engine coolant switch.
Pin5 Ckt570 black/white - was a ground for the AODE's Transmission Control Switch Module (if equipped).
Pin6 Ckt679 grey/black
Pin7 Ckt258 white/pink - not required, but was connected to pin2 of Low Engine Oil Warning Relay.
Pin8 Ckt39 red/white - connect to dash temp gauge (comes from C-104).
Pin9 Ckt11 tan/yellow - connect to tach "signal"
Pin10 Ckt31 white/red - connect to dash oil pressure gauge (comes from C-104).
Pin11 Ckt658 pink/lt green - connect to ground leg of "MIL" lamp (also connected in the harness to C-199 DLC connector).
Pin12 Ckt676 pink/orange - connected to ground at G201, this wire went to pin2 of the Mustang's speed control amplifier, and provided ground for the Mustang's speedometer.

Connector C-216 (male / black)
(12) terminals
Located behind the Mustang's instrument panel, under the RH cowl.
Modifications/connections are required as noted below...
Pin1 Ckt
Pin2 Ckt
Pin3 Ckt
Pin4 Ckt
Pin5 Ckt
Pin6 Ckt
Pin7 Ckt
Pin8 Ckt
Pin9 Ckt
Pin10 Ckt
Pin11 Ckt
Pin12 Ckt

Connector C-259 (female / grey)
(8) terminals
Located near the firewall on driver's side in back of strut tower.
Connector plug is for diagnostic use only, so no modifications are required (wiring details shown for referance only)
Ckt

Connector C-294
(60) terminals
Located near the firewall on driver's side in back of strut tower.
Connector plug is for diagnostic use only, so no modifications are required (wiring details shown for referance only)
Ckt

Connector G-119 (lug)
(1) terminal
Located near the ECA connector in the passenger side kick panel area.
Connector should be attached to chassis ground.
Ckt48 - ignition shield ground

1995 Mustang Alternator Wiring Guide
The back of the alternator has the following terminals, which should be connected to the car as follows...
Ckt38 "B+" black/orange - connect both of these terminals to the battery side of the starter relay.
Ckt4 "S"
Ckt4 "S" white/black - connect these two terminals together with a short loop of wire.
Ckt904 "I" lt green/red - connect to ign switch "start"/"run" thru the "Alternator Warning Lite" (alt warning lite is connected in parallel with a 510 ohm resistor).
Ckt36 "A" yellow/white - connect to the battery side of the starter relay thru a 18ga fusible link.