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: 90,719 (32,000–203,000)
1 model year affected: 2006
35 people reported this problem
22 people shared problem details
2006 Lincoln Zephyr127,000
hard shifting from transmission. hard thump when car is put into reverse after that car has been running for 20 minutes
2006 Lincoln Zephyr90,000
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 Zephyr90,000
Shifts hard when I step on it, also sometimes at lower speeds decelerating.
2006 Lincoln Zephyr87,000
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 Zephyr67,000
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 Zephyr90,000
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 Zephyr150,000
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 Zephyr92,000
Transmission shifts hard when it gets warm. It shifts so hard it feels like it is going to come apart.
2006 Lincoln Zephyr79,000
noticed it after 24 hours of owning. we just try and baby the car.
2006 Lincoln Zephyr55,000
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 Zephyr67,000
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 Zephyr57,000
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 Zephyr120,000
It hesitates when accelerating. It has not been fixed. HELP
2006 Lincoln Zephyr100,000
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 Zephyr32,000
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 Zephyr203,000
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 Zephyr88,297
Same, hard downshift at 35 and 24 mph, worse when warmed up.
2006 Lincoln Zephyr58,000
Will not shift. Can not get up to speed.
2006 Lincoln Zephyr83,000
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 Zephyr130,000
Noticed issue over a year ago. Have been told by a dozen mechanics it could be a dozen different things. Has been going for well over a year with this issue and no complete failure yet.
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