Depends on where you live and what year model you have. I know the 2000 models and maybe some 2001 models only have 1 catalytic converter per side, where the 2002-2004 models have 2 per side. On the early models you will completely lose your cats if you go with headers and may not pass inpection of they do any kind of tail pipe testing or visual inspection where you live. On the later models you will keep your secondary cats and can usually get away with headers most places.
As for factory replacements that will also depend on what your stock ones look like. Some models had exhaust manifolds and primary cats that were all one piece where others had ones where the primary cats were bolted to the exhaust manifolds. Just need to make sure you get the right ones.