Hey Don, can't speak to the ram air but I have run K&N filters and Piper Cross which is like the ram air style So I figure the ram air is fine also. when it comes to pipes you first need to figure out whether your going to stay will the three pipe look or not. If so and you can find or have a set of TORS I would add the three pipe cat delete as you will notice more. This does not mean you can't add the TORS first as your cat box is empty but you would gain a wee bit more power and sound without it. The newer Roadster went to two cans which could be added to yours with a little bit of mounting work but I doubt it is any more the the TORS even the two pipe tors. Any exhaust after that will cost if you don't mind dual's you might find a set of Jardines pop up for sale on fleebay every now and then.
Now as for how the headers change with the ports being the same besides the air flow ability the exhaust port in the head push into a pipe do you want them to push into a restricted pipe the size of a garden hose or maybe something larger