I went into a truck performance store today and was told that they recommend leaving the stock pipe in place from the turbo back to the muffler, remove the stock muffler and replace with a 4" high flow model, and connect to the stock piping on out to the exhaust tip. Any ideas whether this is acceptable?

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I think it might be cuz a 4" frontpipe will rub a bit on the cross member. I hear people say that. I will find out soon for myself. 4"frontpipe and 5" back.

4" frontpipe fits just fine with no problems.

Think I am going with the Summit 5" turbo back exhaust. Besides the spare tire issue are there any other interference issues I need to be aware of? I hear that the heat shield at the cab may be a problem.

You should clear the spare by 1/2"-1" no problem.