Remove and clean the EGR valve and passages, then double check the initial timing setting. A sticky EGR valve pintle will cause a brief rattle on acceleration, at an upshift, or up a light grade: usually no ping on hard or WOT accelerations.
Was there any movement of the Throttle Sensor when you replaced the EGR. There's a specific way to reset the TPS with the ISC and throttle at absolute 0, and the battery cable must be removed to allow the ISC to relearn. Call me crazy but I've always replaced the fuel filter on those years after misdiagnosing everything from fuel injectors to fuel pumps. Clogged filters are notorious for gumming up the works.