Dude....sorry, but you're just gonna have to deal with it. I keep telling people that flow-through duals on a stock 3.8 are too much, but all I get is arguments.
bhuff30 has it right.....Not only do the gases move slower due to increased exhaust volume, but they cool down way too fast as well....cold air is heavier than hot air, and therefore slower-moving.....and that kills low-end torque. You may have gained HP on the top end, but your low end has suffered for it.
You can't compare it to a 96 because their stock numbers are way lower to begin with.
You can't have the best of both worlds without doing pretty major mods to your engine. If you want at least SOME of your low-end back, lose the Magnaflows. Go with a restrictive muffler, not an absorption muffler. You'll sacrifice some on the top end, but it'll still be better than stock. It'll sound better too, but that part's just my opinion.
Either that, or put a procharger kit on it. Woot!!!