You might want to get an expansion chamber exhaust pipe from sickbikeparts.com. It's $65, and works great(so I've heard). My pipe got clogged, it doesn't unscrew, so I cut the bottom open, shoved a long screwdriver in the pipe(make sure it goes to the curve in the top). The cat you need to remove is a really tough piece of honeycomb metal welded in there. With a combination of pushing the cat out the top and pulling some out with long needle nose pliers, you should be able to pull the whole thing out.
Or you could just get a performance exp. pipe, or a new stock pipe.
Hopefully you get things worked out!