Parts that have a loose or sloppy fit may knock on start up until a film of oil coats the surface. I'm assuming you did not use forged pistons, as these do slap on startup.
The fact that the noise returns at higher rpm's is disturbing. If it comes to a tear down , before you go to deep pull the front cover & look over the timing chain & tensioner.
Also look for other tell tale signs of a problem, oil pressure readings when hot, use a magnetic oil drain plug, drain the oil & examine the oil & cut open the filter . Check for motor bits, the color and material may tell you whats happening.
good luck