Vibrates when stopping?

Two years ago, the engine was replaced in my 1990 Astro CL ext. van. Immediately this problem started. It runs and rides smooth when moving, but when I apply the brakes at a full stop and sit with my foot on the brake pedal to keep it from moving such as at a stop light, it vibrates so hard that it shakes the whole van. When I take my foot off the brake and accelerate, the vibration stops. Then, when I stop again, it starts again. You can even hear the vibration. Help, no one seems to know what is causing this. I first was told it was the motor mounts, but that was not the case.