I think you got a good deal. It sounds like you found the right shop. I was in the same situation last month. I went to a small custom exhaust shop and asked for everything new and custom bent from beginning to end. He told me everything upstream of the Y looked great. I had the flex replaced a couple years ago. He gave me a nice quiet muffler, a custom bent stainless tailpipe, and a polished stainless tip for $345.
All of these franchise exhaust shops just wanna look up your vehicle in a book, bolt on the parts while you wait, get your money, and get you out the door. Any custom work is a pain to them. You have to look around and luck out with the right manager willing to think outside the book. A small shop where the owner does all the work and can custom build anything is a great way to go also.
Mark
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