i can't imagine anything that has preignition at idle..
To check piston clearance, get a piece of thin electrical solder wire about 6 inches long. Remove the spark plug and stick the wire into the hole. Hold one end of the wire and get the other end to touch the side of the cylinder in there.
Use whatever means to turn the flywheel. You want the piston to go up, squish the solder wire and to keep going past top dead center.
Remove the solder and the end should look flattened. (if not use thicker solder) Measure how thick that flattened part is. This is how close the piston comes to the cylinder head near the edge of the combustion chamber. When things get hot, that clearance decreases..
Side clearance on the lower connecting rod is critical and specs are mentioned in every manual i ever seen.. Don't just wiggle the little end of the rod.. All rods wiggle a little. Use a feeler gauge to measure the clearance between the connecting rod's side and the crankshaft .. down at the bearing.
Another check is up-and-down clearance. This is more likely to cause the noise you describe. I forget the proper method to measure this.. it takes some careful setup.. it's probably on the Net if you do a search.
I didn't know you toasted that motor.. bearings often go away when a cylinder/piston go. I like the sound of this less and less as this thread progresses..