Drivetrain Help with Check Engine Light after Transmission Swap - 1990 Mustang LX 5.0

Here are photos of the connector I found below the MAF. There are 8 wires coming into the connector on the body side and 7 wires plus a blank on the engine side. It looks as though the jumper I need to change is on the engine side and there are two wires side-by-side that both appear to be brown with a yellow stripe. One is directly across from the blank and the other is next to the first one. My guess is that when I unravel the insulation that the 2 brown with yellow stripes are nothing more than a jumper...correct? All I need to do is to pull the red retainer, remove the brown with yellow stripe that is the 2nd one from the end, and relocate it to where the blank currently exists. Correct?

And just to make sure, my car was originally an AOD car with an A9L ECU that I swapped out to a T-5 and kept the A9L processor. So the change in the

jumper is what I need to do, correct?
o2 connector1.jpg
o2 connector2.jpg
 
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Well, I jumpered the O2 connector as per your instructions...very straightforward. Then I did an OBD 1 test, but with the engine cold. I immediately got an 11 (which is good), but then it was followed by a 21-O, 22-O, 23-O. Knowing that the engine needs to be warmed-up, I realize my OBD-1 test was probably suspect. I disconnected the tester and started the car. Just idling in the workshop, I noticed the CEL was still on and the engine was idling a little rough and lower...between 500 and 600 RPM, but did not stall. I plan to take the car out on the road tomorrow morning, see what happens and rerun the OBD 1 test.
 
Do a computer reset, disconnect the battery for 30 min with the headlight switch on, turn head light switch off and connect the battery, drive it around running various engine speeds and driving conditions then run the codes.
 
I will leave the battery disconnected and headlights on overnight and in the morning, turn off the headlights, connect the battery and take if for a half hour drive, then return and run an OBD 1 test. Thanks for your help today!
 
There are 2 ways the signal ground inside the computer can be damaged.:

1.) Wrong O2 sensor harness, which is the rabbit we are currently chasing.

2.) Jumpering the diagnostic test connector to the wrong single connector.
Foxbody Diagnostic connector close up view
foxbody-diagnostic-connetor-closeup-view-jpg.586765


The STI has a gray connector shell and a white/red wire. It comes from the same bundle of wires as the self test connector.

WARNING!!! There is a single dark brown connector with a black/orange wire. It is the 12 volt power to the under the hood light. Do not jumper it to the computer test connector. If you do, you will damage the computer.
Both wires are visible in the picture,

This is a common newbie mistake and it is easy to do.

This is crucial: the same wire that provides the ground to dump the codes provides signal ground for the TPS, EGR, ACT and Map/Baro sensors. If it fails, you will have poor performance, economy and drivability problems
When the Check Engine Light is on, the computer is running in limp mode. Limp Mode uses a preset configuration built into the computer firmware. It protect the engine from damage, but give reduced performance and economy.
 
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Here's my accomplishments so far today:
1) I checked to make sure I am using the correct single lead for OBD 1 testing and I am. The single lead connector is gray in color and comes out of the same loom as the multi-pin connector that plugs into the back of the OBD 1 tester.
2) I drove the car for a little over an hour...all types of driving, from city to highway, slow to fast, and full-out. The CEL was illuminated the entire time so I'm probably in limp mode. If that's the way limp mode runs, I hope I'm in limp mode as I get older. The car ran like a banshee!!! The idle definitely improved on its own and has a nice 600-700 RPM idle at rest.
3) When I returned to my shop, I re-ran the OBD 1 and came up with the following KOEO codes: 12-O, 23-O, 34-O, 67-O, 85-O, 22-O and 22-C. On the second pass, there was no 12-O, just on the first run through the codes.

Whenever I check codes, I always have to ground the single test lead to get the OBD 1 tester to communicate with the ECU. My guess is that I may have an internal ground issue in the ECU. What if I simply jumper the single test lead to a ground? Will that supply the ground lead that the ECU is looking for? Is it time for me to tear into the dash and remove the CEL bulb? The car is running great and everything works fine other than that pesky CEL! :mad:
 
At this point, I would pull the ECU, clear off the workbench and open it up and look for a burned up pin 46 trace

Edit: actually before doing that. Test for continuity between pin 46 & 60 and then 46 & 40. You should also have less than 1ohm of resistance. No continuity would suggest it’s burned
 
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At this point, I would pull the ECU, clear off the workbench and open it up and look for a burned up pin 46 trace

Edit: actually before doing that. Test for continuity between pin 46 & 60 and then 46 & 40. You should also have less than 1ohm of resistance. No continuity would suggest it’s burned
This is exactly what I have been telling you all along...

The damage to the computer may be the result of a previous owner's efforts. I don't recall seeing that you were to only owner of this car.
 
I do know that the previous owner was the original owner and when I purchased it with 50K miles, had absolutely no modifications. It was like a time capsule, so if anyone may have burned a circuit in the ECU, it would probably be me. My only modifications are a 3.73 rear axle, BBK off-road H-pipe (but the O2 sensors are in-place), removal of the thermactor pump and hoses and elimination of the EGR using the kit purchased from LMR with the resistor pack. Since you've already walked me through the re-jumpering of the O2 harness, can you think of anything else that might cause a circuit to fry in the ECU? What I'm thinking is pulling the ECU, check continuity as suggested by Mustang5L5 and either repair or replace if I find a burnt printed circuit. I don't want to pull the ECU, repair/replace it and reinstall it for it to burn printed circuits again. It looks fairly tough to remove the ECU due to tight quarters. Any tricks to removing/replacing it?
 
Oh, and conversion from AOD to T-5 using the kit provided by NEO Mustangs. I guess my biggest concern is that if I repair/replace the ECU, now that I corrected the jumpering of the O2 harness, is there a possibility the the circuit would fry again? If I pull the ECU, open it up and find the fried circuit that is identified in a previous post, repair it, do I want to try the ECU by laying it in the footwell before reinstalling?
 
OMG! I just pulled the passenger side kick panel and saw that the ECU is stuffed in there pretty tight, Almost looks as though the dash needs to be removed...or at least the HVAC components on the passenger side! Nothing in the Ford shop manual about how to remove the ECU...Yikes!
 
It’s not that bad. You don’t need to pull the dash. Just remove the kick panel. Unplug it and slowly work it down. It’s tight but it does come out and go back in.

also, let’s pause for a second. This car is an original AOD car right? But you said it had an A9L? (Manual trans ECU) but it appears this is your first time pulling it out.

how do you know it’s an A9L, and who put the a9L in??

let’s slow down because this info is very important in knowing how to proceed. The jumper change was made with the assumption you have an A9L in there because you told us that.
 
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Holy Cow...this just gets deeper and deeper! It's definitely an A9L (I attached a photo below). Sorry that the photo shows somewhat of a reflection on the top of the "A". This was definitely an AOD car as I checked the VIN tag to verify. I pulled the CARFAX that I purchased before buying the car and it shows that there was one previous owner prior to the guy I purchased it from. The fellow I purchased it from would not know an ECU from an accordion, plus he gave me all the receipts he had for the car. Some new paint, a convertible top, tune-ups, oil changes, etc. but nothing really mechanical or electrical. Carefully studying the ECU and its ground plus adjoining connectors and wires, I'm positive the ECU has not ever been removed. No witness marks on screws, etc. Everything I've touched on the car makes me feel that I'm the first to have touched it since it left Dearborn Assy. This is the processor that was in it when I was running the AOD with no CEL, even after I removed the Thermactor and EGR components. Ideas?

A9L Processor.jpg
 
A couple of things that a Ford insider would know:
1) The Ford part number with the prefix E9ZF would designate a 1989 design, consistent with the fact that this is a 1990 car.
2) Its definitely not a service part because it would have had a prefix where the "F" would be a "Z" as the "Z" is the release character for Customer Service Division.

So, it looks like an original production part...
 
Well, I have some more interesting information: I looked on LMR's site and it says that the ECU code can be found on the ECU located behind the passenger side kick panel. I looked (and photographed) and it is A9L. LMR also said that, if you're lucky, the white tag may still be on the passenger door jamb with the processor code. Mine's there...and it reads A9P. Attached are photos of both the door jamb sticker and ECU. What the heck is going on? If this is truly a manual trans. ECU, how did it function without a CEL with the AOD? Any other thoughts or should I start trying to pull the ECU?

A9L Designation.jpg
A9P Designation.jpg
 
A9P is the automatic ECU, so somebody put an A9L in there. With the jumper being correct you just now need to see if that one is fried.

another question to ask. When you put the 5spd trans in, did you have a plug for the NGS on top of the T5? Did you plug it in?

reason I ask is because an AoD car won’t have this plug for the NGS, so you would have nothing to plug it into unless you change the trans harness to a manual one. (Which you should do)
 
Yes, the T-5 rebuilt transmission kit from NEO Mustang (Northeast Ohio Mustang) did include the NGS that I installed on the top of the transmission. I remember it well because the trans. was shipped to me without the switch and It was shipped to me separately (with the little pin), so I had to install it. Unfortunately, I already had the transmission installed so it was an absolute nightmare to access! The kit came with a brand new harness that replaced the auto. trans. harness. I recall that the harness had connectors for the fuel pump relay (under the drivers seat), VSS, reverse light switch and the NGS on top of the transmission. I remember having to connect the harness to an existing connector behind the drivers side kick panel. All connectors were correct and I installed them all. Did I do right or wrong? I guess I'm wondering how someone might have installed an A9L ECU into an AOD car and not trip the CEL, especially when the O2 harness was in the configuration for an AOD setup?