98 Sunfire Transmission

I have a 98 Sunfire that had a new engine installed around 2,500 miles ago. About 3 weeks after this, I started having a problem where my car starts shaking slightly when it idles at a traffic light or stop. It got significantly better on its own, and has gotten worse in the past week to ten days. A couple times today even, when accelerating up a slight incline, the car would be very slow to accelerate.

Can anyone help?