The length of the pipe TOTALLY effects how the engine will run and perform. Generally, the longer and more restrictive an exhaust system is, the better the low end torque will be. As you shorten the pipe and free up the flow within the catalytic converter/muffler, you will start getting more mid range and top end torque. This is why you see a lot of drag cars that have down turned exhaust that exits before the rear axle, sometimes as short as the back of the doors. This is to get as much flow as possible at high RPMs. There is a science to exhaust tuning, but it's all about what you want out of your engine. For the 2" you cut off, you will probably get a slight increase in your mid range torque, but I don't think 2" is a drastic enough change to have to worry about retuning anything.
Scottie