Take out the inline muffler(resonator) and change stock muffler to a performance muffler for a few extra horsepower(5-10hp approx). Your exhaust will also sound a lot better. Use a K & N cone filter. It will give around 2-3 hp increase.Buy a performace chip(3-9hp aprox). These are about the cheapest you can do.
Before you mod anything, you should install a transmission cooler. Do a search on this and you're bound to come up with more info than you'll ever need to know on them.
Honestly, the best bang for the buck mod I ever did was having my PCM reprogrammed by American Motorsport . It's around $300 depending on what you want, but there's not many $50 mods that are going to cause a noticable increase in power.
Removal of the resonator is not going to give you ANY performance increase. The resonator is nothing more than a larger diameter pipe welded in, with a relatively precise length to make the exhaust pitch correct. By removing it and putting a muffler in it's place, you're only further restricting the exhaust gases. Bad idea!