I agree with too many/too big holes. The velocity of the gas/air mix in the holes has to be higher than the flame front speed otherwise the flame will burn back into the manifold. Once it does so, the gas in the manifold burns, increasing the velocity of the gas flowing through the orifices and pushing the flame back out. Then the cycle repeats. That's probably what is causing the puffing.
I would look at a gas grill of known BTU output and measure and count the holes. You want to provide about the same on your burner if you are hoping for the same BTU output.