There are emissions controls in the manifolds, then there is the main catalytic converter, and then there is your resonator and mufflers. But it all depends on which element is not working (throwing the CEL)
If I were you (depending on which element of your emissions controls is broken), I'd simply get a new cat, and some MIL eliminators. The main catalytic converter is all you need to pass emissions and be environmentally friendly. And the MIL eliminators will get rid of your CEL from the manifolds.
Your other options are to pay the 2 grand and get all factory parts (huge waste of money IMHO), or you could get some MSDS headers and y pipe and a new main cat!
Good luck!!
Bridge