Or your piston could be hitting your head. I had it happen once when I first started playing around with lowering the cylinder deck. I lowered it just a CH too far & although the engine still ran very well there was that noise. I remember that it was louder when I wasn't moving & I had the clutch in. That's what leads me to think you may be experiencing the same.
Was the rattling noise preset at all before took off some of the head? Pull the head off and check to see if there's any contact points on the head & cylinder.
If it is hitting you can try adding another head gasket to see if that solves the problem. Of you could try adding another (or a thicker) base gasket. This will change the timing though, and it may not be exactly what you're looking for.
You'll never know until you try though. Good luck getting to the bottom of it.