First, I'll state I'm not a Gen 2 fan. I'm not bashing Gen 2's, they're just not for me. That being said, you've apparently had 2 minor issues, the second of which may have been caused by the first.
You had an IWE tubing issue that you were initially unable to diagnose and relied upon the dealership to fix. They kept your truck for 27 1/2 days longer than necessary and fixed nothing, and probably caused the transmission leak when they opened it after falsely determining "the transmission was the issues for front grinding noise". Now you have an ongoing transmission leak that may be an easy fix if it's just the pan or stick tube hole (that has no tube).
In total, you have less than $10 in do-it-yourself repairs that could both be fixed in your own driveway on a Saturday morning. You fixed the IWE issue, you could drop the trans pan and reset it.
You bought a "specialty vehicle" (I use that term loosely), you should expect to have to diagnose and make minor repairs. I find I enjoy my vehicles more when I turn my own wrenches. It's not for everyone, but you did the tubing so you are capable.
The place where I agree with you and I would lose my mind is that they will keep a new $75k vehicle for any period of time with a problem under warranty that they are unable to diagnose (correctly or incorrectly), and not give you a loaner. Ford customer care and service is horrible... I tell everyone that.
