Transmission Noise problems of the 2005 Mercury Mariner

I purchased a 2005 Mercury Mariner in March of 2007, this vehicle had 11,000 miles on it. In June of 2009, I begin hearing rattling noise in the engine and the gears begin operating very poorly. Had an auto shop check out what the problem could be in June of 2009, and was told my transmission needed repair. I stopped driving the vehicle and begin using a rental car until I could put the money together for the repair, which I was quoted over $2100. 00. I contacted Ford to inquire about why I'm having this problem at 40,989 miles, Ford claimed they had no reported cases of my mechanical problem and that I needed to get it to the dealer to be checked out. I was informed I would be responsible for all charges, repairs, towing and rental car expenses, since the 36,000 miles warranty and 3 years had expired. I made arrangements for my car to be repaired by the first auto shop, and the transmission was rebuilt, total coast, not including rental car came to $2237. 50. July 16, 2011 I was traveling approx. 30 miles and my od off light begin flashing, made a stop at a convenient store, restarted the car and the od off light had stopped flashing. While continuing to travel approx. Another 30 miles, od off light begin flashing again, approx. 20 minutes later the check engine light came on. There were no signs of over heating, no strange smells of any sort, the vehicle continued to run as normal. Once I made my final designation, the vehicle appeared to be fine and normal, still no signs of over heating or no strange smells. While traveling back approx. 45 miles, the od off light begin flashing, no signs of over heating, no strange smells. Approx. Another 30 miles, the check engine light came on. Check engine light remained on, I located a coupon for a free scan with aamco, which found that my transmission need to be repaired, the transmission fluid was drained and was burnt. Total cost for this repair, not including rental car is $2290. 00, mileage is at 59,900.