I have a 2000 Honda Civic EX and it is making a ticking/ knocking noise from what seems to be on the bottom end but I know something on the top end can sometimes echo throughout the block. This only happens at idle and when it's warmed up. It goes away after 1.5k rpm. I took off the oil pan and everything seems to be fine, changed the rod bearings while I had it off, set the valve clearance to spec, I even put some thicker oil in it to see what would happen and no change. I'm stumped to say nun the less. My compression numbers are fine too, 175, 175, 175, 180. No metal in oil either. If you know or have had this problem, please help me figure out what it could be!!! Engine is a D16Y8 with 181k miles on it.

 

What you're saying sounds a lot like what was happening with my car when the vtec solenoid was stuck on, there was a little Rock in it, I'm guessing my dog walked over it when I had the head off