The car is a 92 Civic LX sedan with an automatic transmission and D16Z6 engine. I put this engine into the car a couple years back because the original engine threw a rod. After putting it in I noticed that there was a loud rattling/clanking kind of noise coming from the engine bay when I would drive the car. The noise would only happen when I would go past about 30% throttle so I simply drove it with the gas pedal pressed less than that 30% so that I wouldn't hear the noise. I figured it was a transmission problem but today I noticed that the noise also happens when I quickly blip the throttle and it seems to be coming from the engine. This is really concerning me now because it is a pretty nasty noise to be coming from a motor. I read that it could be the heat shields on the catalytic converter but I don't think they're the problem. The noise sounds like it's coming from the head or bottom end. Don't know if this might be related but I also noticed that the harmonic balancer is wobbling(the bolt is tight so I guess the harmonic balancer is bent) and there seems to be an oil leak coming from the LH side crank shaft seal. Also, there's no a/c compressor on the car so the noise isn't related to that. The engine sounds fine at idle and sounds fine if you smoothly bring up the revs so it puzzles me that the noise only happens when accelerating medium-hard and when I quickly blip the throttle. Any ideas?

 

An inexpensive engine stethoscope, a pair of jacks, and a buddy's help should solve the mystery.