2006 GT SMOG Test Woes - "Modified Software" and PCM Removal


KevinMar

New member
Mar 26, 2021
4
Los Angeles, CA
Good evening everybody,

We've owned our '06 GT for 15 years now, and bought it from its original owner. The original owner was a friend of ours and had the car modified by Speed Gallery where they fitted the Whipple 4.0L blower, an "850hp" tune, and removed the catalytic converters (but left the stock exhaust??).

For several years we were able to somehow get the car SMOGed just fine. But not wanting to deal with the incredible smog shop that had worked so well for us in the past, we wanted to return the car to a state which could pass the test anywhere.

We took our car to Kendall Pond who reinstalled stock catalytic converters, and swapped out the stock exhaust for a Heffner straight pipe to keep it sounding good.

Great! We thought, time to get it SMOG tested. FAILED

For some reason the readiness monitors had been reset at some point and we had to do the typical drive cycle. We got this done and verified it with an Autel OBDII reader.

Second SMOG test. FAILED

Reason? "MODIFIED SOFTWARE. Your vehicle failed its Smog Check inspection because the vehicle's computer software does not match an accepted configuration."

Ok well, the car is tuned, so this should easily remedied. We had the SCT-4 tuner and we'll just revert the car back to the "stock" profile which is saved to the SCT-4 unit. Got that done, did the drive cycle again, and took the car back to the shop.

Third SMOG test. FAILED

Same reason, modified software. This didn't make any sense to the SMOG test employees, so we inquired with a Ford dealership and they said we may need to "clear the cache in the ECU." The logic here is that even though the "tune" currently loaded on the PCM is the stock configuration, the SMOG system is still picking up remnants of the modified software, or can tell that it has been modified in the past. "Clearing the cache" will reset any telltale signs of modification.

Well it's a good thing I own a FORSCAN tool. I plug that in and look for a function which matches what the dealership described. I cleared the PCM codes, refleshed the "stock" tune, did another drive cycle, and went back in.

Fourth SMOG test. FAILED

Ok now to why I'm posting here. With all of these attempts, nothing has worked. This has left us with several options, but none of them very attractive. The one which I am currently pursuing is the replacement of the PCM with a new unit from Flagship One.

After poking around the engine bay, I found the PCM, but wasn't sure how to remove it. I pulled out our Workshop Manual and on 303-14-18 they explain how to remove the PCM, however they don't show exactly how you're supposed to access the PCM electrical connector bold, or the lower PCM cover bolts.

Finally the question, is there any easy way to remove the PCM without removing bodywork?
 

69b302

GT Owner
Mark II Lifetime
Mar 13, 2021
115
Upstate NY
I believe aftermarket tuners leave some indication the car was tuned by a non OEM method. Have you tried having Ford reload the stock tune?
 

nota4re

GT Owner
Mark IV Lifetime
Le Mans 2010 Supporter
Feb 15, 2006
4,281
Kevin, as I have said before, I don't think that the PCM swap is the right solution and is just going to add more stress to this saga. Despite what you read or perhaps hear from the seller of the PCM, I do not believe a tune file will be in the PCM... and even if something's there it is NOT coded to your car's VIN. I think this is another rabbit hole you don't want to explore.

Re-loading the stock tune-file into the GT doesn't appear to be working. I believe the following are your 2 best paths forward.

1) You can remove the Whipple and replace with an OEM SC and then take the car to a CARB referee. They should be able to approve the car.

2) You can leave the Whipple and re-load the Whipple tune file that the car has had all of this time and take the car to SMOG station or referee (a referee may be required) and provide them with the Executive Override #d-231-29. This is the CARB-legal certification obtained by Whipple. This is completely legitimate (Whipple DID get their set-up approved) but the wording on the EO is very poor as it tries to cover several cars that Whipple got approved.
 

twobjshelbys

GT Owner
Jul 26, 2010
6,189
Las Vegas, NV
Chances of a stock tune being operationally compatible with the Whipple are low. My car wouldn't operate until I returned the MAF and throttle body to stock
 

nota4re

GT Owner
Mark IV Lifetime
Le Mans 2010 Supporter
Feb 15, 2006
4,281
Chances of a stock tune being operationally compatible with the Whipple are low. My car wouldn't operate until I returned the MAF and throttle body to stock
Not sure why you had trouble but we have done this a dozen or more times. MAF sensor isn't changed with the Whipple (not sure why yours was?) and the car doesn't know a whipple is sitting on it instead of the OEM SC. Of course, one should never venture into boost with this arrangement but the car will run/drive fine with the OEM tune file and a Whipple.
 

twobjshelbys

GT Owner
Jul 26, 2010
6,189
Las Vegas, NV
Not sure why you had trouble but we have done this a dozen or more times. MAF sensor isn't changed with the Whipple (not sure why yours was?) and the car doesn't know a whipple is sitting on it instead of the OEM SC. Of course, one should never venture into boost with this arrangement but the car will run/drive fine with the OEM tune file and a Whipple.

My setup was a pulley/tune from GT Guys. It changed the MAF to a Mercury part number and the tune disabled all of the O2 sensors, the EGR and one other "readiness" test. The MAF change was perhaps instead of the level shifter thingie? Also colder plugs. Anyway, the car wouldn't run with factory tune without the factory MAF but none of the readiness OBD2 tests would come on until I put the factory tune back. I was able to get emissions to pass without the pulley (but never "got on it" with it in place) but eventually put everything back to factory before I sold it. The guy Rich had do it tried several iterations but never seemed to understand even though I sent tons of pictures of the OBDII tests. I finally threw my hands up and went back to factory. I wished I had just got the Ford Racing Parts tune which was 50 state compliant...
 

KevinMar

New member
Mar 26, 2021
4
Los Angeles, CA
Kevin, as I have said before, I don't think that the PCM swap is the right solution and is just going to add more stress to this saga. Despite what you read or perhaps hear from the seller of the PCM, I do not believe a tune file will be in the PCM... and even if something's there it is NOT coded to your car's VIN. I think this is another rabbit hole you don't want to explore.

Re-loading the stock tune-file into the GT doesn't appear to be working. I believe the following are your 2 best paths forward.

1) You can remove the Whipple and replace with an OEM SC and then take the car to a CARB referee. They should be able to approve the car.

2) You can leave the Whipple and re-load the Whipple tune file that the car has had all of this time and take the car to SMOG station or referee (a referee may be required) and provide them with the Executive Override #d-231-29. This is the CARB-legal certification obtained by Whipple. This is completely legitimate (Whipple DID get their set-up approved) but the wording on the EO is very poor as it tries to cover several cars that Whipple got approved.

I hear you, I was not discounting your advice in any way. As you know, my name is not on the pink-slip. I am only acting as the in-house service provider for the registered owner, so his wishes take precedent. This thread was merely a last ditch effort exploring the PCM swap avenue.

The concern with the referee path is that they may find something else wrong with the car (such as the Heffner exhaust) and require us to fix those "issues" before signing off.

If you don't believe this is legitimate concern, then I will begin going down the referee route.
 

KevinMar

New member
Mar 26, 2021
4
Los Angeles, CA
Chances of a stock tune being operationally compatible with the Whipple are low. My car wouldn't operate until I returned the MAF and throttle body to stock
While the car clearly felt detuned, and I wouldn't feel comfortable going WOT, the car was perfectly drivable with the stock tune and Whipple SC.
 

nota4re

GT Owner
Mark IV Lifetime
Le Mans 2010 Supporter
Feb 15, 2006
4,281
My setup was a pulley/tune from GT Guys. It changed the MAF to a Mercury part number and the tune disabled all of the O2 sensors, the EGR and one other "readiness" test. The MAF change was perhaps instead of the level shifter thingie? Also colder plugs. Anyway, the car wouldn't run with factory tune without the factory MAF but none of the readiness OBD2 tests would come on until I put the factory tune back. I was able to get emissions to pass without the pulley (but never "got on it" with it in place) but eventually put everything back to factory before I sold it. The guy Rich had do it tried several iterations but never seemed to understand even though I sent tons of pictures of the OBDII tests. I finally threw my hands up and went back to factory. I wished I had just got the Ford Racing Parts tune which was 50 state compliant...
Ugh... enough to sour anyone on the pulley tune set-up. Not sure if there were growing pains or what with the tuner but I'd say we installed 50-100 "pulley/tune" kits (for cars being exported to Mexico, of course) and NONE were this complicated.

Even a tuned car will spend 90% or more of its run time in closed-loop mode relying on the upstream O2 sensors feedback to maintain a pretty flat 14.7:1 AFR ratio. If these upstream O2's were truly disabled, the car would be in open-loop continuously which really wouldn't make any sense. I HAVE seen tuners turn off the downstream O2 sensors and suppress the cat efficiency test, but this too is completely unnecessary. Suppressing the EGR - while perhaps healthy for the car (but not the environment) is also unnecessary. Even when States used rollers and a brief drive cycle while measuring emissions at the tailpipe, these drive cycles would keep the car in closed-loop mode the entire time - guaranteed.

Well developed pulley/tune kits from Torrie who, in my opinion, is at the top of his game - don't do any of these stupid things. Torrie's tunes would routinely pass CA emissions (remember, he's not changing ANYTHING that effects closed-loop operation) so emissions would be identical to an OEM GT. (This is EXACTLY how Ford Racing was able to get CARB certification... they too knew what they were doing.) Unfortunately, CA Smog test now routinely looks at the tune file and compares it to stock and will flag a car with anything other than an OEM tune.

Back to Kevin's problem.... we've reverted DOZENS of GT's back to the OEM tune file and we've never had a problem getting the cars to pass the smog test.
 

nota4re

GT Owner
Mark IV Lifetime
Le Mans 2010 Supporter
Feb 15, 2006
4,281
I hear you, I was not discounting your advice in any way. As you know, my name is not on the pink-slip. I am only acting as the in-house service provider for the registered owner, so his wishes take precedent. This thread was merely a last ditch effort exploring the PCM swap avenue.

The concern with the referee path is that they may find something else wrong with the car (such as the Heffner exhaust) and require us to fix those "issues" before signing off.

Pursuing another PCM will cost you time and $.... and has a very, very small possibility of resolving the problem. As I am thinking about the problem.... are your sure your car hasn't been flagged??? Maybe you ARE getting a good (OEM) tune file into the PCM but each time you go to the smog shop - he's just getting feedback from Sacramento that your car has been flagged. There ARE offenses where only a visit to a referee station can clear them.
 

twobjshelbys

GT Owner
Jul 26, 2010
6,189
Las Vegas, NV
Ugh... enough to sour anyone on the pulley tune set-up. Not sure if there were growing pains or what with the tuner but I'd say we installed 50-100 "pulley/tune" kits (for cars being exported to Mexico, of course) and NONE were this complicated.

Even a tuned car will spend 90% or more of its run time in closed-loop mode relying on the upstream O2 sensors feedback to maintain a pretty flat 14.7:1 AFR ratio. If these upstream O2's were truly disabled, the car would be in open-loop continuously which really wouldn't make any sense. I HAVE seen tuners turn off the downstream O2 sensors and suppress the cat efficiency test, but this too is completely unnecessary. Suppressing the EGR - while perhaps healthy for the car (but not the environment) is also unnecessary. Even when States used rollers and a brief drive cycle while measuring emissions at the tailpipe, these drive cycles would keep the car in closed-loop mode the entire time - guaranteed.

Well developed pulley/tune kits from Torrie who, in my opinion, is at the top of his game - don't do any of these stupid things. Torrie's tunes would routinely pass CA emissions (remember, he's not changing ANYTHING that effects closed-loop operation) so emissions would be identical to an OEM GT. (This is EXACTLY how Ford Racing was able to get CARB certification... they too knew what they were doing.) Unfortunately, CA Smog test now routinely looks at the tune file and compares it to stock and will flag a car with anything other than an OEM tune.

Back to Kevin's problem.... we've reverted DOZENS of GT's back to the OEM tune file and we've never had a problem getting the cars to pass the smog test.

My car ran great and passed Colorado emissions tests but it was a tailpipe sniffer at idle and it passed with flying colors. They hadn't done OBDII testing (it started with later model years) and they also wouldn't run the full dyno test due to the high horsepower.

However when we moved to NV we had the OBDII readiness method of emissions testing ...

NV follows CA emissions but lags a couple of years so I can predict that we too will have the originality factor coming soon.

PS. There was some speculation that the tune I was given was intended for a twin turbo or cat delete configuration because of all the OBDII tests that were disabled. I don't know all I know is I was never able to get it to work and wasn't getting anywhere with the tuner and was trying to get the car ready to be sold so I just reverted to the factory config for everything.

It is worth nothing that changing the tune file also resets all of the OBDII readiness indicators so you have to run the full drive cycle. I got pretty good at getting it done with minimal miles. We were allowed one "not ready" and in Vegas the hardest one to get is evap due to the temp it wants to run at.
 

KevinMar

New member
Mar 26, 2021
4
Los Angeles, CA
Back to Kevin's problem.... we've reverted DOZENS of GT's back to the OEM tune file and we've never had a problem getting the cars to pass the smog test.

Pursuing another PCM will cost you time and $.... and has a very, very small possibility of resolving the problem. As I am thinking about the problem.... are your sure your car hasn't been flagged??? Maybe you ARE getting a good (OEM) tune file into the PCM but each time you go to the smog shop - he's just getting feedback from Sacramento that your car has been flagged. There ARE offenses where only a visit to a referee station can clear them.

Yeah we're not pursuing a new PCM at this point. It seems like the only way forward at this point is through the referee.

There's no way to know if the car has been flagged based on the SMOG reports we got. Are there any recommended referee stations in West LA? Is it your recommendation to keep the CARB certified Whipple tune on the PCM and not worry about the Heffner exhaust? Our worst case scenario is the referee finding a new reason not to pass us.
 

nota4re

GT Owner
Mark IV Lifetime
Le Mans 2010 Supporter
Feb 15, 2006
4,281
Yeah, I would go to the referee with the Whipple tune... and have a printout of that EO number I gave you. The exhaust shouldn't be an issue as it is clearly AFTER the cats. (What you do with the "clean" emissions post-cats is your business.) I think the biggest challenge is the poor wording by Whipple on the EO document. Its kind of like a patent where the submitter is trying to use the broadest language possible to limit any infringements. In Whipple's case, they are trying to cover several make/model cars with that one EO and it gets a bit confusing. What you do have going for you (as if the TRUTH counts anymore), is that this really is the EO that was approved for the GT.