Sorry for your difficulties. Well I drive a 1998 Civic DX, basically the same engine.
A 98 Civic LX does not have EGR.
I suspect some of your changes are the cause. You are missing a downstream O2 sensor? Isn't there a CEL lit on your dash? You have a non-standard exhaust header and mods to the electronic controls. All these and the new tires are sources for the possible losses in MPG. And despite confidence in your standard driving technique, our butt dynos are just too imprecise and too vulnerable to confirmation bias. Fuel changes, driving changes, colder weather... all could be producing or contributing to this decline.
I don't agree that narrower tires will have higher rolling resistance than wider. The contact patch on wider tires is larger. Did you buy LRR tires? Let the tires break in.
I hope some of that is helpful. Keep posting updates...
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See my car's mod & maintenance thread and my electric bicycle's thread for ongoing projects. I will rebuild Black and Green over decades as parts die, until it becomes a different car of roughly the same shape and color. My minimum fuel economy goal is 55 mpg while averaging posted speed limits. I generally top 60 mpg. See also my Honda manual transmission specs thread.
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