transmission options and questions
I believe the 09 engine with have VVT, so that might be some extra complexity that you may or may not want to tackle. The only real good way to make them work so far is the factory computer, but the factory computers on those cars are tied into so many other systems that it can be tough to separate all the systems. I know there is some VVT development going on in aftermarket computer systems, but I think it's still in its infancy, so it might not be the most complete or capable system.
For what it's worth, my T56 swap probably ran me around $2500-3000 all told. That included the transmission, bellhousing, and clutch parts to make it all work. I know that it's tough enough to handle just about anything I want to throw at it as well. There was a bone stock one sitting in a 1000 whp Viper in the local club for several years.