While the factory y-pipe is restrictive, replacing it without headers really doesn't show much of a gain, if any. The Magnaflow Ypipe is only about $30, but most shops are going to use cheaper aluminized steel with crush bends anyway when making your new one. In the end, I would just leave the Y-pipe alone unless you are going to be adding headers. If going with longtubes, they all offer a mandrel bent stainless Y-pipe to go with the header...this is going to replace the majority of the restriction in that factory system.
As for the muffler, you may pick up 5-8hp with a free flowing muffler, but that is tough to feel in the seat of the pants. The muffler will be more for sound than it will actual performance gains. Longtube headers are where the power is at.