Shorty headers do nothing so scratch them off the list. If you want to retain that factory cats keep what you have.
With longtubes, you are going to have to remove the factory cats. You will then have to get a "shorty" H or X pipe. That can be either catted or catless. Just know that you are going to lose at least two of the factory cats (four total).
If you really want to keep the factory cats (the most restrictive part of our exhaust) at least have a shop remove the Y-pipe and make your exhaust true dual.