Shaking and making weird noises

Ok, i have a RWD automatic w/ overdrive, I got a transmission put in it about 2 months ago, it shifts fine, but when i stop or press the brake the car shakes, vibrates, and screeches, and the engine is a lot louder than it used to be. Please help me figure out whats going on with my car.....

Sounds like a brake job and a muffler should be next on your list...