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I've owned a couple Civics of that generation and worked on friend's vehicles as well. I don't remember my LX having an EGR valve... The only ones I remember having an EGR is the EX. Also, if your ECU was setup to be using EGR, it would throw an engine code if it didn't see one. So, I think your replacement engine has an EGR valve when your original did not.
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