Need Some Advice

We have a 92 chevy truck 4x4 just had Chevy put in brand new 350 motor got new ignition module & coil everything is basically new except for the ECM & EGR Valve but the EGR valve is working properly because we tested it the pickup runs/idles rough when ya just first start it but after driving it, it does okay till it sets again like overnight.. Really big bummer especially after gettin a new motor put in & haven to put more money into it please help??????