Intake noise???

2004 CBR1000RR air box has been gutted, pair mod, micron full exhaust, power commander 164.88 map, my question is when you romp on the throttle hard from around 4000 rpm, you hear a loud noise coming from the front of the bike, it doesn't do it or as noticiable from higher rpms, is this common with the airbox opened up?

Yes.

its definately annoying! Would an aftermarket intake like an atec make a difference?

It may help , it's still going to be louder than stock.