Update:
They will be receiving another x-pipe from StainlessWorks tomorrow. This will be the third x-pipe they have tried to get the fit perfect. Keep in mind, this is a one-off exhaust set-up right now, but after they get mine done StainlessWorks will be putting their 4.0 Longtube exhaust set-up on the market.
Brian said that as long as the x-pipe fits tomorrow... they will finish the exhaust, dyno and tune it again, then install the supercharger and gears... then finish with a final dyno tune.