So...this whole thing turned out awesome!
I had an extended warranty. The dealer were I take my truck to to keep up on the maintenance, etc. so that my extended warranty will be covered, neglected to tell me about the 30 and 60K transmission flush. The extended warranty people asked to see those specific records, before they authorize a rebuild of the transmission. The service manager verified that they did not ask on the flush and figured the right thing to do is to make it good with me. So, I got a re manufactured transmission from Ford with a 5 years 100,000 mile warranty on it, new transmission cooler, flushed the cooling system and replaced the fuel filter for $617.00. I only paid the difference between the cost of the re manufactured transmission and what the extended warranty was going to cover on the rebuild (parts+10 shop hours @ $100.00 an hours). So...I can't complain!