The manufactures do many things to their engines year to year. What you'll need to do is make sure the engines are EXACTLY the same. This means ALL sensor are in the same place. All the injectors are the same and the engine isn't more powerful. Because your old computer won't know how to run an engine with different power specs. It'll try to feed the new engine the same fuel/spark as the less powerful engine and it won't work.
Also, you'll need to make sure the transmission from the new engine is the same as yours, because the computer controls both.