I wanted to thank you all for your advice. I didn't win this one, and ended up trading this vehicle in. I am losing sleep over this because I have a conscience and there is a good chance someone is going to pick this up off of a lot and end up with a problem.
I called Ford customer service directly and they did put in a negative feedback which they said would be reviewed by Ford and the dealer. This whole ordeal has really left a bad taste in my mouth and it will probably be a long while before I end up considering another Ford. What really got me here was the service advisor and his condescending demeanor. He was 100% against me before the problem was even looked at. On top of that it's obvious he's used his misinformation on unsuspecting folks before and that is downright WRONG. A large amount of people depend on those folks for their expertise and to mislead them for the sole purpose of the $$$ is just crooked. The salesman (Tim Pundmann) has been one of the best I've ever worked with, but at the end of the day he didn't help much either.
Just in case anyone ever comes across this again I thought I'd share what I found. I spent a large amount of time over the weekend with a blacklight looking over the engine and trying to track down the dye. I was able to clearly find it and the path it was taking down to the bell housing. Everything is very tight in there, so it is difficult to say exactly where the source is, but it appears that it was coming from the head gasket itself. I'm going to try to snag some screen shots from the Ford Parts website and highlight it, but I believe that it was leaking on the upper corner of the rear head (as you are facing the engine). When you are under the vehicle, there is only a small window where you can see the back side of the cylinder head right above where the bell housing begins. I was able to get a Q-Tip up there and take a swab of what I believe was the dye. Once I was able to get my hand back out, I was able to put the Q-Tip under the black light and confirm that it was. I could clearly see with the blacklight where it was running down the curved edge inside of the bell housing with the inspection plate off. I am almost certain that it wasn't from the main. The rear valve cover was also seeping all the way around as well.