Are you just replacing the muffler or are you doing a complete cat back setup? I would go with the 2.5" pipe with any new exhaust. Also know that the regular 40 is louder than the 40 delta flow which I and many other members use.
Hmmm... I don't remember the size of the stock pipe because I fully replaced mine. Maybe be 2.25 then. Hopefully someone else that did what you are looking to do will know better.
Tarheel, you will need 2.25 center out and 2.25 in. The inlet position wont matter as a shop will have to make you an inlet pipe. Place the muffler at the tail pipe inlet, to the rear of the cab. For less drone in the cab