DD16 2020 intake throttle issues

have a truck in deleted, and strait piped, egr is still active. while driving loaded or unloaded the throttle valve and egr valve open and close rapidly causing the truck jerk around. (feels like you are on and off throttle rapidly. gets really bad then suddenly clears up for a couple hours then comes back. have check tune and all seems well there. have changed throttle valve and egr valve. still there, now if we remove the intake throttle valve plate truck runs amazing but shortly throws a code for the trottle valve and derates. can any one let me know how to program the throttle plate out of ecm if possible? its like the egr and throttle valve are fighting each other...