Nowdays with junkyards charging an arm and a leg for everything, and with the dropping prices on SE V-6 type M/T cars, you are actually far, far ahead to just SELL your car (removing your expensive parts of course), and buy another that has the desired options already installed. Back in the 60s, 70s, and 80s it was no big deal to swap engines and transmissions, but nowdays, they are so deeply integrated into the computer systems on the car. You would get weeks, and weeks tied up into the swapping, and it would cost a ton for all the little parts that are also different (needed to make it work). Sorry, I'm not trying to discourage you in a bad way. I've done swaps of this caliber before. I've put a 5.0L FI engine into a 4 cyl Mustang before and many others, and it might have been worth it back then, but now, in this day and age, it's just not worth it. Goto
http://www.autotrader.com and just check out the VAST selection of Contours for sale, cheap!