If memory serves, is there not a clear coat over the factory stripes so there are no "ridges" between car color and stripe color? This would be much harder to do than just applying stripes. I have no top stripe so I can't check mine. Definitely would affect resale, Shelby at Elite would probably have an answer as to an amount. If the cars hits the right buttons for you and it's in your price range, go for it. Just know that if you decide to sell, it will be an obstacle.
Good luck!