Hard for me to say if its normal or not. Most likely it is. Deleted trucks with performance tuning are louder than stock. The trucks I've heard run with the Ultra never rattle excessively.
Having said that, monitor your injection timing and actual rail pressure. Tell me what you see at idle, at cruise, during average acceleration going through the gears... and tell me all this in relation to engine rpm. Knowing this will tell me if it is spot on.
BTW, plugging the servo motor for the EGR back in shouldn't effect rattle.
Ray
Double R Diesel, LLC
www.doublerdiesel.com
info@doublerdiesel.com