Custom exhausts usually don't have stainless piping unless you request it and then they charge you more. The way they bend the pipe also is a big factor in the price, most pre-made exhausts should have mendrel bent where as some shops don't do it this way. A full kit actually had time put into the design and placement of bends and at a local muffler shop they probably just guess and throw it up there. I don't know about the warranty on a custom exhaust but most full kits have a good warranty. The labor at your local muffler shop is probably people who didn't do well in school or minorities so they charge less.