91 honda civic dx?

Well, let me tell you a bit about my car, when I bought it, it ran perfectly, but a few weeks later I checked the muffler and it had a hole about 8 by 8 inches wide and long. The car ran perfectly so I didn't think anything of it, and just recently, I was driving it down the interstate, and all of a sudden it seems like it lost a lot of power and it starts off really slow at a stop. There are black fumes coming from the car where the muffler is, but it never had that problem, even when it had the hole in the muffler until just now. I thought it would be the fuel filter due to the loss of power and takeoff. I changed the fuel filter and when I dumped the gas from the old fuel filter it was a real dirty brow color. When I installed the new fuel filter, the car seemed to be running better, but still has that slow takeoff problem. What I also forgot to mention was that the car starts to shake a lot in park and I feel it shaking underneath the car. Please help and thank you