03 Lincoln LS Transmission/ PCM Issue after Sending to SIA

Layla11242

Layla11242

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Hi everyone, I'm hoping somebody can give me some tips on the next steps to take with my 03 LS.

A few months ago, I had sent my PCM to SIA Electronics for repair because the car was shifting very hard 3-4th gear and sometimes reverse. It was a little over a 3 week wait. Anyways, upon my first drive with the repaired PCM, I could tell that those problems were fixed, but not I had a brand-new problem- the car will randomly downshift really rough (about 10% of the time). Once the car downshifts rough like this, when I go in reverse, the car will keep engaging and disengaging reverse within seconds of each other, resulting in the car going really slow and slamming every few seconds. I've also lost 4th gear entirely one time. I'm gonna guess that this is a PCM issue considering that this never happened before I sent it to SIA and started immediately after I got the PCM back. The issues will go away if I turn the car off, then back on.

I called SIA about this, and the tech had said that my PCM may have a bug, and to get it reprogrammed/ updated at a ford dealer/ locksmith. I've called my local ford dealer and they have no idea what a PCM update is.

Should I call another dealer or locksmith to try to get the PCM reprogrammed? I've also heard that dealers can be risky when it comes to PCM work. Is there any DIY/ cheap steps I can do to narrow the list of possibilities?

I appreciate any insight on this

(Not sure if this is worth mentioning but I got a tune by Torrie about 10K miles ago, not sure if this has anything to do with it. I returned the car to stock tune this week and it had no impact on the issue other than reverse not slamming as hard.)
 
Layla11242 said:
A few months ago, I had sent my PCM to SIA Electronics for repair because the car was shifting very hard 3-4th gear and sometimes reverse. I
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This sounds like the notorious valve body/solenoid pack issue. If the milage on your LS is around 130k miles, it may be time for a new solenoid pack.

Warning: stay away from any/all "rebuilt" solenoid packs on eBay. All they do is make adjustments, and call the solenoid pack "rebuilt".

There are other issues with the 2003 LS transmission, depending on date of manufacture. Some of the LS transmissions got bad transmission fluid that was lacking a friction modifier.

That led to some 2003 transmissions having a short lifespan. Call your local dealer and give them your VIN #. They should be able to tell you if yours has the modifier in the fluid.

If not... then you may be looking at getting the transmission rebuilt, which opens up another can of worms.

Sorry for the bad news, but you are a little late in the game at this point.
 
Thanks for the info
The transmission was rebuilt just 40k miles ago by a pretty reputable shop. I heard about the 03's issue with the fluid and solenoids, but I had disregarded it because the transmission was rebuilt, so I had assumed the solenoids and fluid are new.

I will get the solenoid pack replaced and get back to you. Although I'm still worried about the PCM. SIA was able to fix the 3-4 shift issue by "repairing" the PCM. On top of that, my new issue started immediately when I got the PCM back. Also, the issue with reverse only occurs when the car downshifts incorrectly but fixes itself when I turn the car off then back on. I also asked SIA about the possibility of it being the solenoids and the tech said that it's not likely, and to just get the PCM software update.

I've heard info about a software update for these cars, specifically for shifting issues, although my local dealer seems to have no clue what I'm talking about.

I'm not trying to argue your response at all- I know you have a lot more knowledge about the LS than I do, I just wanted to add some more info to see if that changes any possibility, especially now that I have conflicting recommendations. Assuming this info doesn't change anything, I will replace the solenoid pack.
 
I would not replace anything until you run the codes?
Yes it does sound like a valve body problem but at this point we don't know.

Post back with what you find.
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.
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Hi troubled 03 ls owner, please read
www.rv.com

Tranny Filter Tech

Tranny Filter Tech: Keep Your Automatic Transmission Alive (Almost) Forever.
www.rv.com www.rv.com
before you decide on any coarse of action.

Screenshot_20240720-104316_Chrome.jpg
 
@Layla11242 if its not the coils or the solenoid packs i would check the electric motor on you're throttlebody. The silver housing that slides over the electric motor has magnets glued to the inside of it and if these magnets come unglued and get slightly out of place they will throw the electric motor out of balance and create problems that could cause you to think its something else. Immediatly after having my transmission rebuilt i was driving down the road and it went into ETC fail safe mode. I took my throttlebody apart and after finding those magnets loose and seeing where that electric motor had been hitting against them for quite some time, i believe its what caused my harsh shifting problems. My car would bang hard when shifting from park to reverse, it would go into nuetral and bang back into drive when turning to fast or braking quickly.
 
Buckie said:
it would go into nuetral and bang back into drive when turning to fast or braking quickly.
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Sounds like your transmission is low on fluid. The 5r55S tranny typically holds 6-7 quarts of Mercron V.

Eight if you also have an inline filter.

Since there is no dipstick... there is a specific procedure for getting the fluid level correct... per the LS shop manual.

If you continue to drive with low fluid, you risk permanent transmission damage.
 
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04_Sport_LS said:
Sounds like your transmission is low on fluid. The 5r55S tranny typically holds 6-7 quarts of Mercon V.

Eight if you also have an inline filter. Since there is no dipstick... there is a specific procedure for getting the fluid level correct... per the LS shop manual.

If you continue to drive with low fluid, you risk permanent transmission damage.
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I wish i was still having problems outta my LS lol but it was rear ended back in January and is setting in my front yard now with a salvage title. But to what you said about low fluid. I had the fluid checked when it was doing all the rough shifting and it was full. 2 weeks later i pulled into Walmart and when i came back out. It wouldnt move a inch. I had it rebuilt after that. And thats when i found the problem with the throttlebody.
 
I suggest you get the car (level) on stands and pump an extra quart of fluid into the transmission. There is a small plug in the center of the tranny drain plug used to fill the transmission.

If you can get the small plug out and fluid doesn't run out, you may be low on tranny fluid.

I hate to beat a dead horse. but the shop that rebuilt the transmission, may not have put enough fluid in the transmission.
 
SteveOwens said:
Thanks for your story on a bad thottle body!
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Your welcome. I took a throttlebody off of a 06 Ford Explorer and swapped those motor housings and it never acted up again. I guess that glue gets hot or maybe the glue was not as good as it was supposed to be and those magnets turn loose inside there. I wish i could've found that before i had my transmission rebuilt. I might have saved that $2200.00. Since the wreck in January it sets in the yard and i can not decide if i wanna find a clean title LS and swap my engine and rebuilt trans over or just sell mine to someone for parts. The motor has 169,000 miles and runs great. The rebuilt trans has 20,000 miles on it. I drove it home after the wreck , still runs and drives great! Bt the Insurance company totalled the car because the damage got into the back passenger quarter panel.
 
Try adding a dip stick hose to the pan with a quick drain 1/8 npt plug. The pump filter setup is to mount on the ps rack bolts under the rear engine. A Lokar AOD 36" dip stick kit fits well. The dip stick receptacle is 0.8 drill in thick wall pipe. I sent the pan to Pat Garrett at LevelTen Transmissions for his approval before he sent the "Beast" 5R55S with it installed back to me.

20230520_142946.jpg
 
04_Sport_LS said:
How do you know the fluid level was checked properly... and by whom?
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I took it to Superior Transmission and they checked it. When it finally broke 2 weeks later i took it back to Superior and had them rebuild it. Immediatley after having it rebuilt i was driving down the road and one of those magnets inside that housing fell down and wedged itself against the electronic throttlebody motor to where it couldnt move anymore and it went into ETC Failsafe mode. Thats when i found the magnets loose and the electronic throttlebody motor had been wobbling and hitting the magnets the whole time. Might sound crazy but i am convinced thats what caused all that rough shifting until the trans finally broke. I have drove it for 3 years and 20,000 miles since then and no problems whatsoever. If it wasnt for getting rear ended by some kid id still be driving it.
 
Well... the only reason I'm being so persistent about low tranny fluid, is that the symptoms you speak of suggests low fluid.

With low fluid... hard stops, starts, and turns will cause the fluid to slosh around and suck air... instead of fluid.

Case in point...

I have a 1995 F-150 with 240k on the odometer. I drive long distance for work sometimes.

At one point I was driving to work... and the tranny dropped out of overdrive randomly, then dropped back in. It consistently did that for a couple weeks or more

I thought it was an electronic issue, but after checking the tranny fluid I realized the tranny was low on fluid.

This is talking about a truck that holds 16 quarts of fluid... and has an extra deep pan, taking the total to 18+ quarts.

Point is... the truck was losing line pressure because of low fluid.

Don't assume anything.
 
And I'm going to assume that the tranny shop looked up how many quarts of tranny fluid the LS takes... but that's only to the point of checking the level while the engine is running.

If nothing trickled out after 6 quarts, the transmission was still low on fluid.
 
Hi everyone, I really appreciate all the feedback and info.

I just want to clarify that I do not have any CEL. The car hasn't been in failsafe mode either. I only have a simple SCT scanner, not sure if those can even see transmission issues.

I checked the tranny fluid and there was fluid when I pulled the plug out.

The transmission was replaced by the previous owner so I'm really not sure about the filter.

I also want to clarify that this is not the regular "rough shift into reverse". I only have issues with reverse after the car downshifts rough (which is about 10% of the time). In the same drive after the harsh downshift occurs, reverse will go through a 1-2 second loop of engaging and disengaging over and over, although more recently it has felt more like just a double engagement after I reset the car back to stock tune. I also want to make clear that this issue started on my first drive after putting the "repaired" PCM back in the car. The repair has fixed the initial 3-4 issue I had before, and now made this new and worse issue.

Is it worth draining the fluid in case there's debris inside? I've read a lot of info about tranny issues, but I can't seem to find one just like this. I was really hoping that SIA was right and there was just a software update to fix it.
I don't have a ton of $$ to try everything, but I appreciate any feedback :)
 
04_Sport_LS said:
And I'm going to assume that the tranny shop looked up how many quarts of tranny fluid the LS takes... but that's only to the point of checking the level while the engine is running.

If nothing trickled out after 6 quarts, the transmission was still low on fluid.
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Yes they did everything right. And thanks to people like you and Joe and many others on this forum i made sure to ask many questions that people who are not familiar with the LS wouldn't know to ask. I asked how many LSes 1st and 2nd Gens they had rebuilt to make sure they mentioned weak springs and wore out servos and anything else that could cause problems. The Superior Transmission where i live has a great reputation. Thats why i let them rebuild it instead of the other places around here. I been working on vehicles myself since i was 15 years old and thats how i was able to find the problem with the throttle body. You just can't beat them old 5.4s i have a 02 F150 with 270,000 miles and i do all the work on it and its still running like a champ.
 
Layla11242 said:
Hi everyone, I really appreciate all the feedback and info.

I just want to clarify that I do not have any CEL. The car hasn't been in failsafe mode either. I only have a simple SCT scanner, not sure if those can even see transmission issues.

I checked the tranny fluid and there was fluid when I pulled the plug out.

The transmission was replaced by the previous owner so I'm really not sure about the filter.

I also want to clarify that this is not the regular "rough shift into reverse". I only have issues with reverse after the car downshifts rough (which is about 10% of the time). In the same drive after the harsh downshift occurs, reverse will go through a 1-2 second loop of engaging and disengaging over and over, although more recently it has felt more like just a double engagement after I reset the car back to stock tune. I also want to make clear that this issue started on my first drive after putting the "repaired" PCM back in the car. The repair has fixed the initial 3-4 issue I had before, and now made this new and worse issue.

Is it worth draining the fluid in case there's debris inside? I've read a lot of info about tranny issues, but I can't seem to find one just like this. I was really hoping that SIA was right and there was just a software update to fix it.
I don't have a ton of $$ to try everything, but I appreciate any feedback :)
Click to expand...
At this point I will say you might want to go back to a stock "tune" and see what happens.

The typical issue with the solenoid pack is 3rd gear gets locked up and doesn't release until almost a complete stop... with accompanying "clunk"/thud" sounds.
 
There are definitive electrical tests for electrical problems, but not for mechanical issues with the solenoid valves. I think that it is most often a mechanical problem.
 
Hi everyone, just thought I'd post back here for anyone viewing this thread in the future. The throttle body, tranny fluid, coils and solenoid pack are all good. Checked/ replaced. Big $$$. Didn't fix the issue :/
 
For grins, try DeoxiT D5, on the all the electrical connections from the middle PCM connector to all the tranny electrical connections. You may swap harnesses also. Did you verify the pcm to your 03 ?

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