The rear exit doesn't match the stock exhaust exactly bend for bend over the rear axle. Stock - the exhaust runs stacked on top of each other as it goes by the spare tire. The stainless works - the exhaust runs side by side, which puts it into the spare tire.
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http://www.fordraptorforum.com/showthread.php?p=792816
I had to tweak and peak mine a bit to get it right. Probably less than a half inch from my spare. It doesn't get hot enough that far back for me to be concerned and I probably won't have the spare underneath anymore.
I've come to the conclusion that nothing aftermarket will ever fit 100% perfect like a stock part. Even removing a stock part and putting it back may not yield the same results as before. Especially with the exhaust, there are a lot of various pieces that can be rotated to alter the fitment and position. Adjusting the first 90 off the headers by 1/4" can change the position at the ass end by over an 1".