I doubt the engine was really hurt by the fuel filter, other than not being able to run good. Might be a good idea to get the injectors cleaned.
If the fuel filter went so long without being changed, you you should probably check the PCV valve, too. It was probably never changed either.
The black plastic thing sounds like an intake resonator and can be removed with no problems. There is also a res in the wheelwell, and directly above the throttle body. A CTA intake will get rid of all the resonators.
You have one resonator between the cat and the muffler. It looks just like the rear muffler. Removing it and putting straight pipe will get you better throttle response and better gas mileage. Mabye a little more power. Thats the result I got when I took mine off. I didnt get much of a difference in noise.
Taking off the cat will cause a check engine light at the least, and isnt a good thing to do. IMO I would not do it.
