Glad things worked out for you. I have to agree with some of the others on selling the tractor and getting something else. My gut feeling is that it will never completely be the same and issues could arise down the road.
Also, this thread illustrates the reason I will NEVER take anything to a dealership for any kind of work. I have never met a dealership mechanic that I thought was truly competent. Almost everything we've taken in in the past has ended up either with other issues or unneeded work done. I even stand by this for warranty work. I do it myself and just suck it up on the price for parts, knowing it will be done right if I do it.
With that said, (and I don't want to sound like I'm blaming him) I bet if the OP had just let the tractor sit in his shop for a few days while he thought about the problem (or asked advice on here) the whole dealer issue could have been avoided, problem fixed, and he'd still have a like new tractor.
I do agree that the dealer made good on it by not charging anything, I'd definitely buy another tractor from them, but I'd never set foot in the service dept again.