Rotating the S pipe is the way to do it. You can do it yourself and then have a muffler shop weld it up, I don't like clamps!! Another suggestion is using the Walker BTM, unlike the stock muffler that necks down to 2.5" and causes a huge restriction. The BTM is a straight shot 3.5" so all backpressure is gone. There is coming a day, sooner than y'all think, where diesels will have to go through emssions testing in all states. The first part of the test is a visual, when they don't see a muffler you fail. I have done trucks both ways, straight pipe and BTM, and I see no difference in EGT's. The straight pipe is a bit louder. I paid $40 for the BTM and then paid $50 to have it installed after I showed them how to do it, the BTM is HUGE!!! I did the BTM and AIS intake at the same time and between the two my EGT's dropped 100-150 degrees. Add the muffler now or later it's your choice.
Good Luck
NCH
PS, I hope all those who have ripped their CAT's off had the sense to save them!! Mine didn't come with one so I am good to go!!