DGPMinistry
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I have a 2006 Lincoln Zephyr that we have owned for about three years. It has the Aisin F21 six speed.
To keep things as short as possible, I will leave out a great amount of detail. Six months after owning the car, I am on I-81 in a construction zone. Someone messes up merging into traffic, and I give it a liberal dose of throttle. It basically goes into neutral, and "flares" - no MIL's at all. Very scary, 400 miles from home. Drift down to about 55, and transmission comes back in. Continue home without any further trouble.
Almost a year later, coming home from a training class for work, the car goes into 3rd gear, sets off the "yellow wrench" and MIL light. Do some looking for answers online before I take it to dealer where I bought the car - find the TSB on the valve body/solenoid pack needing replacement and PCM reprogram. I pay the dealer over $3k to do this work. It does the trick...until three months later. Three hours from home, in Lynchburg, VA, car jerks hard and goes into limp mode, sets off both lights, and is in 3rd again. Get it to the hotel, jerks hard into reverse and I park it overnight. Borrow local parts store's code reader - P0979, Shift Solenoid C fault. Clear code, drive car all the way home without trouble.


Take it back to dealer, they tell me it is "locked up in third" and I need a new transmission! They refuse to fix it, but don't refuse to charge me around $90 for hooking up code reader and lying to me about condition of car. I use some sort of "rewards" points that my tranny repair (earned?) me during the last fleecing, and hop in the car. And it goes home...30 miles away WITHOUT FAULT!
Ask local mechanic for help, and he refers me to ex-Ford specialist (free-lance, out in his own garage). He finds two coolant lines leaking because of Orings being RTV'ed and re-used.
RTV is also inside tranny and on valve body...stuff is everywhere! They routed the internal harness wrong, putting strain on wiring. Fixes all this stuff...and problem goes away! 
During state inspection, another mechanic finds bad transmission mount. Engine was moving around a great deal. I think this also may have contributed.
One year later, out of the blue, car throws code 0979 again. Had tranny flushed, found more RTV bits. Replaced other tranny mount. Drive for a few miles, pull into a parking lot, go to put it in drive and it shudders. MIL's are back - stuck in third. Get it home. Let it sit. Next day - back to normal! I drive it for a week...no problem going 10 miles round trip to work and back. Stop and go traffic, some hills, cruising speed...no trouble. Take it to church - 30 miles there and back. No problem. Figured it was okay...
Load the car up to go to Gatlinburg, TN for the weekend. Get gas 15 miles from home. I start up put it in drive, get a small shudder! No lights then. Thought I was being paranoid, so I get on 81. Go 10 miles, I get the MIL's...then the car does something weird. I have no accelerator. If I push the pedal down, it stays going one speed. If I let up at all, it drifted down. If I floored it, the speed stayed where it was. Get down the nearest exit ramp, and then it shudders. I'm in third. Over 30 miles from home. I take the service roads back to my brother-in-law's, get everything transferred into his Camry, and we are on the road again. 3 hours later.
When I get back 5 days later, we get in the car and drive it home. That was 7/7/14, ten days ago. Since then, I have driven it to work and back, as well as to the dealership I bought it at. I went to trade it in. They tried to put me in an overpriced MKZ (2007).
I wound up going home in my Zephyr - which we still love a great deal!
Ok, I know this is too long. Here is the punchline:
I call another dealer, 45 miles away. The service advisor was fantastic, and she mentioned that the problem may not lie in the transmission, but the throttle body! If it gives off a bad signal it can trigger the "Limp home/default mode". The symptoms line up with that theory. I have spent the past 2-3 weeks on the 'net reading all I can about the Aisin 6 speed...it has to be that, or I suspect an intermittent harness failure.
Any thoughts on this? Hopefully I will have more info soon. I have a service appointment on 7/24, and will share any info that I can to help anyone else having problems!
To keep things as short as possible, I will leave out a great amount of detail. Six months after owning the car, I am on I-81 in a construction zone. Someone messes up merging into traffic, and I give it a liberal dose of throttle. It basically goes into neutral, and "flares" - no MIL's at all. Very scary, 400 miles from home. Drift down to about 55, and transmission comes back in. Continue home without any further trouble.
Almost a year later, coming home from a training class for work, the car goes into 3rd gear, sets off the "yellow wrench" and MIL light. Do some looking for answers online before I take it to dealer where I bought the car - find the TSB on the valve body/solenoid pack needing replacement and PCM reprogram. I pay the dealer over $3k to do this work. It does the trick...until three months later. Three hours from home, in Lynchburg, VA, car jerks hard and goes into limp mode, sets off both lights, and is in 3rd again. Get it to the hotel, jerks hard into reverse and I park it overnight. Borrow local parts store's code reader - P0979, Shift Solenoid C fault. Clear code, drive car all the way home without trouble.



Take it back to dealer, they tell me it is "locked up in third" and I need a new transmission! They refuse to fix it, but don't refuse to charge me around $90 for hooking up code reader and lying to me about condition of car. I use some sort of "rewards" points that my tranny repair (earned?) me during the last fleecing, and hop in the car. And it goes home...30 miles away WITHOUT FAULT!
Ask local mechanic for help, and he refers me to ex-Ford specialist (free-lance, out in his own garage). He finds two coolant lines leaking because of Orings being RTV'ed and re-used.


During state inspection, another mechanic finds bad transmission mount. Engine was moving around a great deal. I think this also may have contributed.
One year later, out of the blue, car throws code 0979 again. Had tranny flushed, found more RTV bits. Replaced other tranny mount. Drive for a few miles, pull into a parking lot, go to put it in drive and it shudders. MIL's are back - stuck in third. Get it home. Let it sit. Next day - back to normal! I drive it for a week...no problem going 10 miles round trip to work and back. Stop and go traffic, some hills, cruising speed...no trouble. Take it to church - 30 miles there and back. No problem. Figured it was okay...
Load the car up to go to Gatlinburg, TN for the weekend. Get gas 15 miles from home. I start up put it in drive, get a small shudder! No lights then. Thought I was being paranoid, so I get on 81. Go 10 miles, I get the MIL's...then the car does something weird. I have no accelerator. If I push the pedal down, it stays going one speed. If I let up at all, it drifted down. If I floored it, the speed stayed where it was. Get down the nearest exit ramp, and then it shudders. I'm in third. Over 30 miles from home. I take the service roads back to my brother-in-law's, get everything transferred into his Camry, and we are on the road again. 3 hours later.

When I get back 5 days later, we get in the car and drive it home. That was 7/7/14, ten days ago. Since then, I have driven it to work and back, as well as to the dealership I bought it at. I went to trade it in. They tried to put me in an overpriced MKZ (2007).

Ok, I know this is too long. Here is the punchline:
I call another dealer, 45 miles away. The service advisor was fantastic, and she mentioned that the problem may not lie in the transmission, but the throttle body! If it gives off a bad signal it can trigger the "Limp home/default mode". The symptoms line up with that theory. I have spent the past 2-3 weeks on the 'net reading all I can about the Aisin 6 speed...it has to be that, or I suspect an intermittent harness failure.
Any thoughts on this? Hopefully I will have more info soon. I have a service appointment on 7/24, and will share any info that I can to help anyone else having problems!