All in all, more exhaust gas flow produces more horsepower. However, more exhaust gas velocity produces more torque. It's all about a balance (stay with me as I try to explain).
Let's look at what will be REQUIRED for you to do this exhaust system and still pass emissions, for starters:
Functional Catalytic Converters (at least two or three, depending on stock design).
Muffler that is not uncomfortably loud.
Now- for catalytic converters, a lot of people have had good luck with the Catco brand. For the price, they're probably your best option. They'll provide better flow and, in many cases, better fuel atomization than stock equipment. You'll have two O2 sensors between the exhaust manifold (or header) and the catalytic converter (one on each bank). This will read the initial oxygen levels in the gases exiting the combustion chambers.
Then, the gases get to the catalytic converters. After passing through the cats, they'll hit your second sensors, often called wide band sensors, which also read oxygen levels, but on a different scale. They'll expect the mixture to be different because of the extra gases burning in the cats. Without cats, your sensors will throw a code, tripping your MIL (Malfunction Indicator Light). So- we know you'll need some good cats to get the job done, but without running a more free-flowing design, you won't see as much improvement from your exhaust system.
For your muffler, find something that will keep a low note. I've heard great things about the MagnaFlow mufflers. Stainless steel is always the way to go, especially if you'll be launching boats- the aluminized steel will rot away in no time, trust me. There won't be enough difference between one muffler and the next when you're looking to put it on a daily driver. MAYBE 1-3 horsepower, but I'd much rather sacrifice that 3hp and have an exhaust tone I can handle instead of going all out and getting headaches from the exhaust being too loud. Again, spend the money on stainless steel. It's worth the cost now, because you won't need to replace it later.
As far as what size pipes to use:
FLOW = HORSEPOWER
VELOCITY = TORQUE
That may throw you off at first. Let me explain: With more room for the gases to flow, you'll get better horsepower. It flows more freely with an open (wide) exhaust, so it's better for a higher horsepower band. However, you want torque, so you want to shoot for velocity. Torque is produced by the velocity (or speed) of the exhaust gases passing through the system.
If you have the same amount of gases flowing through a 3" system and a 2.5" system, the gases in the 2.5" system will travel at greater velocity, because there's less room for it to expand. Instead of expanding out, like it would in a 3" pipe, it can only expand forward and backward. It's NOT going back into the engine, so it can only expand forward, so that creates velocity. It's a lot easier to design an exhaust system designed for horsepower gains as opposed to torque gains for this reason.
Now- with all that said, I would personally recommend you run this: Clicky
It's designed for low-end torque, while the only other bolt-in stainless steel set-up (which was actually MagnaFlow) appeared to be designed more for horsepower (MagnaFlow had a straight-through design, as opposed to Gibson's chambered system). There is an aluminized steel assembly, just like the one I linked you to, but aluminized parts only carry a 90-day warranty, whereas Gibson keeps a lifetime warranty against corrosion and rust-through on their stainless steel systems. Again, let me say- it's worth it. I'm about to rebuild my entire exhaust system after making the mistake of running Flowmaster's aluminized mufflers (only a year and a half ago) because they've already rotted inside and rattle.
I'd say get the system I referenced (you can bolt it on yourself) and if you want more performance, take it to a shop and tell them you want to replace from your manifolds to the system you bought and you want to run the same size pipe as what's on the new equipment. Make sense?
I hope this helps you out. Didn't mean to write a novel, it's just not that easy to explain how much difference an exhaust system can make on performance. Good luck and let us know what you decide.