If its covered, and it better be, go with the stock SVT replacement motor. If they need to replace CAMs, get SVT cams not standard V-6 cams. Be certain they put in an SVT motor - get documentation, there are differences in the internals. In fact, be sure the dealer is a properly qualified SVT dealership.
If by some WILD technicality its not covered, I think a 3L would be a sweet substitute. Plenty of info & help here in the 3L boards.
Man, it makes me sad when this stuff happens to a Contour. I don't know how well I would handle it if something happened to my SE.
Good luck & READ YOUR WARRANTY PAPERS FRONT TO BACK so you know what you are entitled to under the CONTRACT.