Stalling, jerking and beeping

[Patricio Ugarte]

Hey everyone,

I´m posting this looking to get advise, guidance and thoughts on what you think its the problem.

I've been chasing an ongoing issue with my 2006 Mustang GT (4.6L 3V, automatic, Mexico-spec). I'm not the original owner, and it's clear the car didn't get the care it needed. I've done a long list of repairs—some things improved, but the main issue keeps coming back in different forms.

Symptoms before repairs:
-Engine would completely shut off randomly after the pats light flashed and beeped
-B2103 (PATS transceiver) was active randomly
-High CO emissions – 6 ppm (should be ≤ 1 ppm)
-Rough idle, jerks, excessive fuel consumption, misfires (this happened 1 time), power loss (also 1 time)

DTCs seen:
-B2103 – PATS Transceiver circuit fault
-P2196 / P2197 – O2 sensors stuck rich/lean (Bank 1 and 2)
-P0193 – High input from fuel rail pressure sensor
-P1000 – Readiness monitors not complete (this one always disappears after a few driving cycles).

Repairs done
-PCM (not original) reprogramed by Ford dealership. Its important to say that it currently has an XB model, although this car originally requires an FB PCM. At some point the original PCM was replaced for unknown reasons.
-Alternator rebuilt. Voltage was below 13v when running hot; I even noticed tilting lights
-Battery replaced with correct size and properly secured
-Positive cable reinforced, This finally stopped the random full engine shutdowns
-O2 sensors (pre-cat) replaced – from generic AutoZone to Motorcraft
-All 8 spark plugs replaced – they were very likely factory originals and never changed
-Throttle body cleansing

Symptoms after repairs
-Fuel consumption improved after O2 sensor replacement
-Emissions are now under control (CO < 1 ppm)
-But the jerking and hesitation and PATS beeping still happens randomly...even a "check fuel cap" appears sometimes when it jerks.

I have been using a BlueDriver scanner and most recently a OBDLink MX+ with Forscan Lite...But I'm leaning towards the PCM itself being the core issue. The symptoms seem to shift between systems – sensors, fuel pressure, PATS – even after replacing the affected parts. This makes me wonder if the PCM is unstable, incompatible (wrong model code), or simply damaged despite being reprogrammed by Ford.

 

[DieHarder]

Hey everyone,

I´m posting this looking to get advise, guidance and thoughts on what you think its the problem.

I've been chasing an ongoing issue with my 2006 Mustang GT (4.6L 3V, automatic, Mexico-spec). I'm not the original owner, and it's clear the car didn't get the care it needed. I've done a long list of repairs—some things improved, but the main issue keeps coming back in different forms.

Symptoms before repairs:
-Engine would completely shut off randomly after the pats light flashed and beeped
-B2103 (PATS transceiver) was active randomly
-High CO emissions – 6 ppm (should be ≤ 1 ppm)
-Rough idle, jerks, excessive fuel consumption, misfires (this happened 1 time), power loss (also 1 time)

DTCs seen:
-B2103 – PATS Transceiver circuit fault
-P2196 / P2197 – O2 sensors stuck rich/lean (Bank 1 and 2)
-P0193 – High input from fuel rail pressure sensor
-P1000 – Readiness monitors not complete (this one always disappears after a few driving cycles).

Repairs done
-PCM (not original) reprogramed by Ford dealership. Its important to say that it currently has an XB model, although this car originally requires an FB PCM. At some point the original PCM was replaced for unknown reasons.
-Alternator rebuilt. Voltage was below 13v when running hot; I even noticed tilting lights
-Battery replaced with correct size and properly secured
-Positive cable reinforced, This finally stopped the random full engine shutdowns
-O2 sensors (pre-cat) replaced – from generic AutoZone to Motorcraft
-All 8 spark plugs replaced – they were very likely factory originals and never changed
-Throttle body cleansing

Symptoms after repairs
-Fuel consumption improved after O2 sensor replacement
-Emissions are now under control (CO < 1 ppm)
-But the jerking and hesitation and PATS beeping still happens randomly...even a "check fuel cap" appears sometimes when it jerks.

I have been using a BlueDriver scanner and most recently a OBDLink MX+ with Forscan Lite...But I'm leaning towards the PCM itself being the core issue. The symptoms seem to shift between systems – sensors, fuel pressure, PATS – even after replacing the affected parts. This makes me wonder if the PCM is unstable, incompatible (wrong model code), or simply damaged despite being reprogrammed by Ford.

Need to fix that.. Low voltage causes all kinds of mayhem with these cars. You should have 14.5 - 14.7 vdc across the battery terminals. I'd start by cleaning major grounds (battery negative; engine block; whatever you can see). If no improvement add a ground (4 awg) from a mounting bolt for the alternator to the passenger strut tower. If that doesn't do it I'd source a new battery cable harness (Be sure it's Motorcraft; ~$100 - 150). Get yourself a VOM (Volt/Ohm Meter) if you don't have one.

Finally found the cause of my low voltage - Beware the all important grounds.

 

[Patricio Ugarte]

Thanks for your help and the detailed reply.


I've already done quite a bit: the alternator was rebuilt, a brand new (correct size) battery was installed, and the positive cable was reinforced with an upgraded terminal. That helped — the full engine shutdowns stopped — but I'm still getting random jerks and codes (PATS, O2 sensors, fuel pressure).


I hadn't cleaned the major grounds yet, and I hadn't tried adding the extra ground from the alternator to the strut tower, so I'll give that a shot. I'll also test voltage with a VOM to confirm the numbers across the battery terminals.


Thanks again for the link to the thread — incredibly helpful. I'll update once I've tried the ground improvement.

 

[DieHarder]

Thanks for your help and the detailed reply.


I've already done quite a bit: the alternator was rebuilt, a brand new (correct size) battery was installed, and the positive cable was reinforced with an upgraded terminal. That helped — the full engine shutdowns stopped — but I'm still getting random jerks and codes (PATS, O2 sensors, fuel pressure).


I hadn't cleaned the major grounds yet, and I hadn't tried adding the extra ground from the alternator to the strut tower, so I'll give that a shot. I'll also test voltage with a VOM to confirm the numbers across the battery terminals.


Thanks again for the link to the thread — incredibly helpful. I'll update once I've tried the ground improvement.

One of the best things you can do is get a new battery harness. That should take care of the voltage issue. Check running voltage after replacing it.

About $160 on feebay: https://www.ebay.com/sch/i.html?_nkw=WC-95954&_sacat=0&_from=R40&_trksid=p2332490.m570.l1313

 

[86GT351]

Check all the grounds for proper contact. If needed remove and use some light sandpaper to clean ground and ground contact.

 

[Patricio Ugarte]

Just a quick update. I took the car back to the Ford dealership to have them re-check the PCM and BCM, since both were reprogrammed by them and are still under warranty.

After a more detailed inspection, here's what they found:

The Smart Junction Box (SJB) has visible corrosion and sulfated pins.
The technician described it as "tartar-like buildup" on multiple terminals.
(Photo taken from the copilot side access panel.)


*i´m still waiting for additional details/findings*

Could this be the true cause behind the random stalls, jerks, PATS warnings,check fuel cap, etc. especially during highway drives?

 

[DieHarder]

Yep, definitely can contribute to if not the source of your problems. Need to check the rest of the connectors down there and the SJB for the same thing. Depending on how bad it is you might have to replace the SJB. You can try to clean pins & connectors with electrical contact cleaner and some small brushes. Hopefully that will resolve your symptoms.

That's a lesson learned for the rest of us. The SJB corrosion problem is a common theme and should be on a short list of items to check when strange things start happening with our cars. Especially if the car is kept outside or exposed to challenging environments.

 

[Patricio Ugarte]

I´ll give a try to the SJB and tell you the outcomes...just another doubt...could you please specify which grounds are the ones you suggest checking and reviewing as well?

 

[DieHarder]

I'd concentrate on cleaning up what you found and then retest. Recommend tooth brushes and electrical contact cleaner (use the type that evaporates). Then retest. If symptoms change you're on the right track.

As far as major grounds go there are 3 and a bunch of smaller ones all over the car. Battery negative is connected to the passenger strut tower; and another one that runs down underneath and is bolted to the underside of the passenger motor mount; and a third on the firewall at the back of the engine (woven mesh) that runs down to the back of the engine/trans. The first is easy to get to; the other's not so much. I'd check them to see if they're sulfated.

Then, get yourself a VOM and check running DC voltage across the battery terminals. Should be 14.5 - 14.75 vdc. If not, consider buying a new battery harness. Get OEM Motorcraft. WC-95954

WC-95954 - https://www.ebay.com/itm/2974001768...IzO7NywSZOKMDS3YSHoscmTg==|tkp:Bk9SR7bphPLrZQ

 

[Patricio Ugarte]

I'd concentrate on cleaning up what you found and then retest. Recommend tooth brushes and electrical contact cleaner (use the type that evaporates). Then retest. If symptoms change you're on the right track.

As far as major grounds go there are 3 and a bunch of smaller ones all over the car. Battery negative is connected to the passenger strut tower; and another one that runs down underneath and is bolted to the underside of the passenger motor mount; and a third on the firewall at the back of the engine (woven mesh) that runs down to the back of the engine/trans. The first is easy to get to; the other's not so much. I'd check them to see if they're sulfated.

Then, get yourself a VOM and check running DC voltage across the battery terminals. Should be 14.5 - 14.75 vdc. If not, consider buying a new battery harness. Get OEM Motorcraft. WC-95954

WC-95954 - https://www.ebay.com/itm/297400176855?_skw=WC-95954&epid=235955879&itmmeta=01JXFJ16JKCZ1NE524JCYPN6B1&hash=item453e6e90d7:g:5ysAAeSwbHNoSMNG&itmprp=enc:AQAKAAAA8FkggFvd1GGDu0w3yXCmi1fBnZeTJxPougV80tQ6zR1qFMUZQMftbkEvKmhneQ44GZubBVTJfWBbve1J2fH0DkQF5tS2+fDVjqMJjHytaX54IjL1iVZKumHUSLud3zjkBqWChD3KtmDM3AWOsYdPg0wNPxFN9rxEcM9xuqiHO/BR+ls69X1hDwtAlIDB5cQ7+AHPrMTEOjXLMuivcSLXRuva1YlzD8wtXhqnZ5xS0JODIAz9lQiWO1xa1NVwhYJzbqcneeimuA4CF4q2TC8VhgrAaIGDgB3ag8DRHnBXrwIzO7NywSZOKMDS3YSHoscmTg==|tkp:Bk9SR7bphPLrZQ

Hi!
SJB has clean pins...but I also want to install the positive harness per your suggestion.

However, the option you kindly sent does not ship to Mexico.

Do you think the following one is the right one to get?

Pardon Our Interruption...

 

[DieHarder]

Hi!
SJB has clean pins...but I also want to install the positive harness per your suggestion.

However, the option you kindly sent does not ship to Mexico.

Do you think the following one is the right one to get?

Pardon Our Interruption...

Yes, WC-95954 is the correct one for a 2006 GT. Note the harness will replace both pos & neg lines. Simply match up the connections and install.

 

[Patricio Ugarte]

Yes, WC-95954 is the correct one for a 2006 GT. Note the harness will replace both pos & neg lines. Simply match up the connections and install.

I've ordered the replacement cable, but it looks like it will take about 2-3 weeks to arrive. I'll post updates once it's installed.

In the meantime—and I assume the answer is most likely yes—if I continue driving the car with a faulty positive battery terminal (which gets considerably hot after long drives), am I risking irreversible damage to the PCM, alternator, SJB, etc?

Thanks in advance for the guidance.