My 98 3.0 auto, has a custom exhaust with no mufflers, dual pipes exiting before the tire. MAC CAI, and JET chip. I love the way it runs. So much so, it's in getting a shift kit, 4.10s and a locker.
As for the intake, argue all you want. I tried putting the stock intake on once after the CAI. Hated it, felt like a gutless slug. It doesn't with the CAI. It's because the stock tube from the MAF to the TB is pinched way down in diameter, which starves it for high rpm airflow. The tube on there now is a full three inches all the way across. I supply air to it via a hose going up to the bumper, and two scoops on the hood directly over the filter. My friend Rick, the guy doing the latest stuff, says it's a great running truck, and the new mods will make it even better.
Then I just need to decide if I want to fix up it's looks, or leave it as a beater. Decisions, decisions.