If it was me, I would try to get the car back to stock, intake/exhaust. I have also wondered about aftermarket header/intake improving mpg's, but I know the civic can get great gas mileage completely stock, and it seems most people on here have stock exhaust and intake. My thinking is if you return the car to stock form, you can eliminate the troubles being anything to do with the modifications. Do you live near any salvage yards? If so you might be able to find the parts you need for pretty cheap, the junk yards here in St. Louis usually have a decent selection, and are much cheaper than ebay.
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