I've hear it's the sweep of the wings. I've seen it cause the sim to shutdown due to the violence. If it gets started, the 727 is dynamically unstable. Meaning it will just get worse and worse. Recovery is a standard maneuver on checkrides. However the simple solution is to just slow down. The problem goes away below about .75 mach.
Define the TO rating. I can think of 6 different engine dash number combinations. At an airport 5000 feet up with a temperature of 40c, a dash 7 engine won't give rated thrust and your takeoff numbers will reflect it. At sea level on a 5c day, a Super 72 with a 219-15-219 engine mix will have some more EPR to give you.