Thumb noises coming from the air intek.

I have a 1999 4Runner SR5 252k miles every time I stop it idles a light idle but enough to grab attention, or put it on parking it idles, if i open the hood and open the air intek I can hear a thumb noise coming out it. Sounds like explosions, ive changed the head gasket, spark plugs, fuel injectors, fuel line filter, and spark plugs cables. I did run a smoke detector and found a leak on the manifold and fix it right away. So there is no leaks. Could it be the coils? Do the coils work together ? If and 1 more question does this truck have a EGR valve? Thank you in advance. There is no check engine.