94-04 v6 models had problems with headgaskets blowing and leaky exhaust manifold gaskets, and the coil on plugs as well. all i can really think of aside from people drivin them hard and breaking stuff
actually 94-98 had the problems with head gaskets, 99-04 engine was refined to not have that issue. the 99-04s are definantly known for exhaust manifold leaks due water dripping from the a/c unit onto the cast manifold. As far as everything else goes the 99-04 mustangs are very sound both drivetrain and engine wise. The 94-98's had many problems thats what happens when you redesign.
and i know for sure that at least 99-04 has coil pack not coil on plug so no issues with that. I know the 4.6L v8s have coil on plug though so thats a thought.
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