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Here's the story:

I have a 1995 Thunderbird 4.6l and am having trouble determine the cause of the engine running rough during acceleration. Here is what has been done to the car recently.

I swapped the engine and transmission from a running and drivable car about a month ago ('94 Towncar). I have owned the Lincoln for 6 months and never experienced this problem. In the swap, I choose to swap the oil pans, intake manifolds, and exhaust manifolds (they were all different, well the intake was the same but I wasn't sure if the sensors were). I used new manifold gaskets and torqued them to spec referencing a Haynes manual. I also replaced all vacuum lines except the plastic red/green EGR lines (I did inspect them for damage and wear). I did not inspect the EGR tube or valve in the process (prob should have though).

I drove the car 1200 miles right after completing the swap. It had been about 3 weeks of in town driving with no issues, then it started having problems running rough (bucking, shaking, etc.) during acceleration. If I babied the gas pedal, it runs smooth and it runs smooth while cruising on the highway. Only during acceleration does it have trouble. The first thing I did was check my work on the intake. In the 1200 mile drive, the intake bolts had backed out considerably. I re-torqued them and reset the computer (disconnected battery). I had the codes read when it first began and had a laundry list of codes. I replaced the following parts: MAF, EVR, TC, fuel filter, air filter, spark plugs (autolite resistors), and wires (autolites) and disconnected/reconnected the battery. None of this resolved the drivability issue. I had the codes read again today at Advance and found only a P1407, which is an EGR No Flow Detected code. I know what that means (intake passage clogged, tube, etc.) but I don't believe that would be causing the car to run so poorly (correct me if I'm wrong). The issue occurs while the engine is warm or cold, air temperature is warm or cold, and at any speed.

I also went to a salvage and the guy was nice enough to let me plug in another PCM, test drive the car (didn't have to buy it) and see if that was the issue. It produced the same results.

I was just curious if anyone else had any ideas to solve this issue.

Thanks in advance
 

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Cats appear to be original. The TPS may be original as well (I don't remember changing it ever).

I had considered the cats, but not the TPS. I need to go pick up a multimeter in the morning (im still 1200 miles from my garage, lol). Wouldn't the cats and tps affect it sitting still as well though? I can put it in park and floor it and it has slight hesitation but it doesn't stumble like it does during driving.
 

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The egr system is activated using a solenoid that regulates vacuum to the egr valve....if there is no flow detected it might be a sign that the vacuum line to the egr solenoid or to the egr valve is broken
 

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and the vacuum leak would result in poor engine performance by allowing unmetered air into the engine. I looked at the line today when I replaced the EGR Vacuum Regulator, but not very carefully. I'll remove it from the car in the morning and inspect it for cracks.
 

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Vacuum lines checked out this morning. I removed them, checked for cracks, and covered the holes with my fingers while I blew into the line. It didn't leak.
 

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I also went to a salvage and the guy was nice enough to let me plug in another PCM, test drive the car (didn't have to buy it) and see if that was the issue. It produced the same results.
You dont ever see this these days! Do you think the vibes could be TC shudder? Does punching it to the floor, or heavily increasing throttle make the vibrations stop?
 

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Sorry for delay in response guys.

The problem has been resolved. The car had relatively new coils on it (1-2 years old), so I assumed they were good. I had a friend look at it (fresh eyes) and we ended up replacing a coil. Problem solved. I guess the spark was weak enough to cause problems only while driving.

Thanks for the suggestions and comments.
 

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The P1407 code has to do with the EGR system. Vacuum lines to and from the valve, solenoid and other parts can cause a lean condition which can cause the computer to freak out with the air/fuel it thinks it needs. The rubber lines is a good place to start. Good luck.
 
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