Damn, I am sorry to hear you going through such a tough time. I bought my 05 GT Wagon in January as well. It is always a risk buying a used car, and these cars specifically seem to be harder and harder to find in good shape and have not been thrashed on by people. What was the mileage like on it? Unfortunately you need another transmission, perhaps you can get your old one rebuilt if it is still in good enough shape? Were you told by a Shop that your new transmission would work with your model year? Perhaps you can go back to them and work something out.
Mine has had a few gremlins (i.e., Valve Cover Gaskets, Spark Plugs, few coolant lines ect, ect) pop up but nothing serious so far. I am doing a complete stage 2.5 or 3 in the next month or 2 when the rest of the parts arrive and hopefully it holds up strong.