I went back and read the whole thread again. You described the sound as sounding as if it was in the cylinders, and under a strong load. That sure sounds like spark knock. But, the Civic should have a spark knock sensor which retards the spark just enough to prevent spark knock.
So, if your civic has a spark knock sensor, it could be bad. That's worth checking.
Also, you might try a couple of tanks of premium gas and see if the knock goes away. Premium burns slower and that may be enough to make a difference. Good luck.
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