Engine knock diagnostic suggestions

So, I swapped the stock 2.0 in my '96 Neon for another stock 2.0. While I had the new engine on the stand replacing the timing belt, I found the stock water pump was severely worn, and my heart sank. It was clearly to the point of losing water. The car I got the motor out of was wrecked and had good compression when I pulled it, so I felt good at the time that the motor was fine, but it's never as good as when you can hear one run.

Forging ahead and fearing the worst, I finally finished the install and...it knocks. It's just one knock, engine speed related, and you can hear it thirty feet away at idle. Car drives fair but seems down on power compared to the second-gen neon I'm driving now, which is a heavier car with identical powertrain.

Any guru's know how to tell a rod knock from piston slap from a dead lifter? I don't know how to tell if it's half-engine-speed or not (i.e. cam vs. crank) but a lifter is easy to check. I looked in all holes with a bore scope prior to install, and all looked fine. I have suspects but would like to get to the bottom of it concretely.

Noise seems to get quieter if I drop it into first and let the car drive the motor.

Thoughts? Suggestions?