Harsh or Delayed Shifting of Automatic Transmission on Lincoln Zephyr

The automatic transmission may develop shifting concerns. On lower mileage vehicles, upgrading the software in the powertrain control module (PCM) and the transmission control module (TCM) may correct the problem. As the mileage increases, internal transmission damage can occur. Repairs could involve replacement of the valve body or a complete transmission rebuild. Whenever major transmission repairs are made, it is important to be sure the PCM and the TCM have the latest software updates to help prevent these issues from reoccurring.

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Average mileage: 94,579 (32,000–203,000)
1 model year affected: 2006
39 people reported this problem
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Viewing 1 - 20 of 26 problem details
2006 Lincoln Zephyr 127,000 mi,
hard shifting from transmission. hard thump when car is put into reverse after that car has been running for 20 minutes
2006 Lincoln Zephyr 90,000 mi,
Was told by a lincoln service shop the car needs a new Valve Body. They say the diagnostic report came back without any codes. Problem began with the LED panel on the instrument cluster working intermittently. Then I noticed it sometimes didn't shift smoothly. Finally, there are sometimes clunking noises, and sometimes a different noise when turning. Other times the car drives fine. The care went from having a clean bill of health at 84K to all these problems at 90K. All regular maintenance and oil changes have been done and the car is not driven hard. I understand this is a known problem with Ford/Lincoln transmissions.
2006 Lincoln Zephyr 87,000 mi,
Car will not accelerate when merging into interstate traffic, it hesitates and slowly adjusts. I am afraid a semi will not see me. I am told to see a transmission person. Is there this not a know defect?? I just had to spend $2100.00 to fix this. Frustrating
2006 Lincoln Zephyr 92,000 mi,
Transmission shifts hard when it gets warm. It shifts so hard it feels like it is going to come apart.
2006 Lincoln Zephyr 90,000 mi,
Shifts hard when I step on it, also sometimes at lower speeds decelerating.
2006 Lincoln Zephyr 67,000 mi,
Car skips when driving up hill/or needing to increase speed intermittently. Dealer states no code upon diagnois referred to DTC update. Recommend 'value body' repair and reset codes. Still working to solve problem
2006 Lincoln Zephyr 90,000 mi,
I have problem with my transmission slipping and shifting hard. Now the problems has gotten worse...started experiencing slippage while driving and hesitation in acceleration.......
2006 Lincoln Zephyr 150,000 mi,
Dealer also says it needs a new valve body. This will cost around $2200.00 to fix. I am seeing a lot of people are having the same issue. It has to be a manufacture defect.
2006 Lincoln Zephyr 67,000 mi,
Transmission shifts hard from park to drive, harsh and/or delayed down-shifts when passing, skips when driving in stop & go traffic. The dealer said there was no issue when last checked around 50k miles but did reset shift programming, which didn't solve the problem.
2006 Lincoln Zephyr 55,000 mi,
The transmission is now linking fluid. I noticed about a month ago slow going up hills and stalling when sitting at red light.
2006 Lincoln Zephyr 79,000 mi,
noticed it after 24 hours of owning. we just try and baby the car.
2006 Lincoln Zephyr 32,000 mi,
When down shifting up A hillor luging it slams and goes into neutral type non gear, have to put it into true neutral and let revs. come to normal level and then shift back into drive.
2006 Lincoln Zephyr 57,000 mi,
i had this issue when shifting to reverse it jerks horribly. also when i accelerate and im about to hit 20 mph it jerks again the shift has a delay
2006 Lincoln Zephyr 100,000 mi,
I can't shift into the rear gear it will pop very hard. Even if the car tries to shift n a different gear it will jump hard
2006 Lincoln Zephyr 203,000 mi,
car has a delayed and very hard shift from 1st to 2nd and from 2nd to 3rd. at its worst the transmission will not shift at all at speeds of 50mph or greater.
2006 Lincoln Zephyr 83,000 mi,
2006 Lincoln Zeypher in Columbus, Ohio. The car will not shift out of first gear, it will not excel over 20 mph. Right now it's sitting at a garage where they have quoted me $3000.00 to replace. It ther a recall on this transmission? Purased only 9 months ago in Mayfield Heights, Ohio from a large well advertised dealership. They offer no help. Anyone know a fair, honest transmission shop in Cleveland or Columbus?
2006 Lincoln Zephyr 120,000 mi,
When I accelerate to merge into traffic the transmission skips as if I had hit a pot-hole... feels like it's going to fall apart overtime. I better change cars before this thing deteriorates and all falls apart. I just don't wanna deal with this.
2006 Lincoln Zephyr 78,000 mi,
Whenever I am in low gear it seems to slip or have a harsh shift. Especially on the freeway when there is some traffic and I have to lightly press the gas to keep pace is when it happens the most. One day it got bad to where after I would stop at an intersection it would take long to get it to go and it would rev up unusually high then shift harsh but then the next day it seemed okay it at least not as bad. I also noticed sometimes after starting my car and shifting from park to drive it would jump. I still got to figure out what and how I am going to get this fixed
2006 Lincoln Zephyr 100,000 mi,
Car drives fine then cannot accelerate and have to shut off and start car to drive again. Took months for mechanic to diagnose throttle body and replaced it. Now car jolts when trying to accelerate/merging into traffic or to pass someone. I was on an interstate going 60 or less and car stopped shifting gears somewhere along the way getting on the interstate so I accelerated slowly which is dangerous in 70 mph traffic rpm was getting between 4 and 5 at 58mph so I drove as best I could home under 60 mph until my exit. Starting from stopped mph car accelerates too slowly. Plus I just took my car in to transmission shop and they said they didn't know what is wrong with my transmission. Before that I had to replace a broken motor mount and noticed after that when I put in reverse it stopped jolting. Now it is starting again a week after the motor mount was replaced. I noticed that the car drives smoothly in the morning and starts to act up after 30 minutes or so of driving. Sometimes won't act up for days then acts up all the time. Comes and goes. Frustrating and scary to drive a car like this.
2006 Lincoln Zephyr 200,000 mi,
put it into reverse and it sounded and felt like someone hit me.