You said the problem happened right after the engine was replaced correct? If so bring number cylinder to top dead center on the compression stroke. Remove the distributor cap and see if the rotor is lined up with the number one spark plug wire. It's possible the distributor was installed 180 degrees out.
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when i had a problem with my dad's crown vic, which was similar to the problem you describe, i disconnected the mass air flow sensor. the car ran better because the computer was using default data. it didn't run great but much better. i changed it and everything's good again. it didn't set a check engine light, so it was a little difficult to find. not sure if your system has a maf sensor. is their a check engine light on?
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