I dont think plugging the EGRvalve back in will help the running issues. Pretty sure stock programming checks EGR flow. If there is no exhaust flow thru your egr cooler, it will put the truck in limp mode regardless of whether or not the EGR valve is plugged in.

The only way to run that new EGR-less intake is with tunes that remove exhaust flow thru the EGR cooler from the programming.