I know that I can get a free-flowing muffler for about $100 or so. My main question is the cost of getting it put on to my car? I would assume they would have to cut the bottom of the body to allow the tip to emerge from my SE. About how much is the labor?
Or what would the approximate total cost be?

Take to a muffler shop and get an estimate. That'* what I did.

The SE is the cheapest, by far. A much simpler exhaust setup. Most guys just bend the tips down below the rear skirt instead of doing the cutout.

Will that affect how the muffler sounds (bending tips down), also are there any real gains from a free-flowing muffler without having a cat-back?

The sound should be fine with the tips bent down. Your preference on whether they protrude beyond the rear bumper skirt for looks.

As far as gains.....there are so many things that play into it. What are you after? Torque or HP? I know the muffler itself won't do it all. I did mine in reverse, though. I had the cat done first (out of necessity) then the muffler when I blew the guts out of it....filming my 'whine envy' in the forced induction forum.

Really there are 3 things that play together here. The intake is the first. You've improved yours already. Now you need to let it fart better. A stock cat will restrict and hold backpressure better, but what that equates to in loss of hp, I don't know.

I DO know with the SC, if you stay with the 2.5" exhaust, and go with a high flow cat and performance muffler, you don't lose any torque, and you gain high-end hp. Whether this is true for the NA guys, I can't say, but I'm pretty sure enough guys have done it to give you a good evaluation.

I don't feel my exhaust improvements off the line. I pick them up in the 3-4000 rpm range. I can really feel it during a freeway pass.

Ultimately, if you want to 'open things up', you need to do the intake, cat, and muffler. Not too much, not to little.