Just contemplating the predicament makes my head hurt....
There's only one way I see this actually feasible. Keep the original transmission installed, or get a rebuilt unit.
On the 2011 engine, delete the AFM and the VVT. Get a new OEM camshaft for the engine you just pulled out, and install that. (At that point might as well replace the lifters, timing chain and oil pump while you're at it)
The 2011 is likely flex fuel, which is different injectors. To keep keep it simple, use your old intake, fuel rail and injectors. If you're old engine has the knock sensors under the intake, they do sell an adapter harness to connect to the knock sensors on the 2011 that are on the sides of the block. Same for the camshaft position sensor. They also have an adapter to switch between the two different reluctor sizes. And then just run your OEM ECM and whatnot. Basically you're just fooling your ECM that it's the same engine.
The other route of totally bringing over the engine and transmission along with the ECM, TCM and whatnot..... Is likely time prohibitive and complex when you run into some modules that you can't just program, but will have to be replaced. You're likely talking about 75% of the entire harness of the vehicle being swapped, with splicing in on the other 25%.