To answer the questions directly, for the header we are still waiting. Traveler made a nice piece that retains the stock position of all exhaust equipment. He made it special and might make more for people who want them.
AWR also makes a nice piece, but is questionable on emissions legality.
As far the bottle neck in the stock exhaust, Traveller found that the outlet of the first cat is small, and the down pipe from there is small. After the second cat the exhaust is the stock 2".
So, open up the outlet on the first cat, and put in a full 2" or even a 2 1/4" exhaust from the first cat on, and you will open up the exhaust a lot.
Port and Polish probably isn't worth it yet.
For the exhaust, I kind of covered above, you'd probably be better off going to a pipe shop and having them custom bend the parts you need. Some of the stock pipes are crush bent, not mandrel. Then find a decent muffler you like and slap that in there.
The stock cats flow just fine, you just might want a bigger inlet and outlet on the second cat to accomodate a larger exhaust.
Then going with a decent intake would help out. It also won't cost nearly as much as going forced induction.
If you have questions about the exhaust, talk to Traveller.