I have the MagnaFlow muffler. I like it but it can get a bit loud. I think the general favorite is still Flowmaster for mufflers.
I also have the 3" exhaust. I think you could get away with 2.5" - 2.75" with the same results. 3" will cost a bit more than the smaller sizes so it might be worth the savings. I am assuming this is a custom install. I would also go with mandral (sp?) bends to help airflow and there are some bends that can be removed by the rear right wheel. You can see here
just how the pipe is dropped down a little and about 3 - 4 bends were removed by making more of a straight shot between the muffler and the engine. In short, the sizes you listed should work, but I wouldn't go any larger.
Your already on the right track with the other mods. The pulley, CAI, and chip are going to make use of the exhaust nicely.