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Q:

while running, the car skips and stalls sometimes without warning. on 2001 Lincoln Town Car

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I had fuel pump and intake manifold replaced.
(2) Answers
(1) Comments
look to ignition system. possible air/fuel mix issue. should diagnostic run to confirm or dismiss.
When was the last tune up? Could be a bad coil or bad coil boots. If boots are oil soaked or real soft, it will miss fire in the spark plug tube. I had the same problem, bad coil boots. These motors, 4.6, are bad to get moisture or oil (leaking valve covers)in the spark plug tube.