You can do pretty much anything to an ATX that you can do to an MTX with the exception of an upgraded clutch/flywheel, and no one offers an LSD for the Auto. With engine and suspension mods though you are in the free and clear. But you seriously don't know if it's a 4cyl or a 6?
A good guide for engine mods for the 4cyl can be found
here, and
here. For the V6 the best intake out there is the CPE with the MAFCi, it's just kinda pricy (though in it's defense, it
does provide pretty much double the hp of the next intake down on the list). A guide for the V6 mods can be found
here.