Best bet to locate the problem is with a mechanic's stethoscope. Make sure you listen to the bottom part of the motor. Put the scope on the main bolts sticking horizontally out of the side of the block right above the oil pan when checking for rod knock.
For checking valvetrain, put the scope on the timing cover bolts going into the cylinder heads or the bolts that hold down the intake manifold. You can even remove the valve covers and run the engine, but the cam gears and chains will sling oil all over the place and make a mess so be prepared for that.
A rod knock can sound like the noise is coming from the valvetrain. And it's even louder if you pull off the valve covers. You'll think you have a collapsed lifter or chain tensioner from the way it sounds and how loud it is without the valve covers on. Make sure you listen carefully to the bottom end of the engine to be sure.
You won't be able to see if you've got a spun rod bearing by pulling your heads. You need to drop the oil pan to visually inspect for a spun rod bearing.