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2000 Lincoln Town Car missing/shuddering

I have a 2000 town car with 210k on the motor. Car has been missing and running really rough for a few months. My mechanic has replaced 2 coils based on the check engine lights that come on while on the highway. Each time the car works better for a few weeks and then it starts running like junk again. Between misfires on the highway, to the car shuddering up to highway speed I am at a loss. I recently replaced the intake manifold (it was leaking) and while it was off changed all plugs and coils.
When we reassembled everything the car ran better then it ever had. Fast forward 3 weeks and the check engine light is on again as well as the misfiring on the highway and the shuddering.
I am at a loss and unsure what to do next. Any thoughts?
Thanks
Answers
Have you had the engine checked with a code reader since the reappearance of the check engine light? If not, have the engine code read and fix the problem. Suggest cleaning the mass air flow sensor. This may or may not show-up on the engine code reader; but, if it is not clean or is faulty, it will make the engine misfire as you have described. The new modified plastic/aluminum intakes appear to boost the power of the engine a little and improves the mpg.
Yes extracting the trouble codes is essential to good diagnosis.
If there's no misfire code you might consider the possibility of a faulty torque converter. Converter misbehavior can mimic a misfire very closely.