If you are moving an exhaust from a cable shifter setup to a rod shifter setup, you will need a different piece of pipe to fit around the rod shifter. Rockauto.com has just that one piece of pipe, or there is actually one on eBay right now. The different y-pipe could cause fitment problems. Can you swap the y-pipes so you keep the same one with your Borla? Other than that, they SHOULD be able to just swap over. I tried to do that once and a local muffler shop totally butchered my Borla transfering from one car to another. If I had had the tools, I think I could have made it fit a whole lot better.
Anyway... best of luck.