You may have to swap the ECM as well for the proper one for the new engine.
The Timing set and sensor on these newer 4.7L is not the same as the one you had.
The exhaust manifolds can be taken from the old motor and installed on the new, eliminating the need for fabricating an adapter to fit the exhaust. Also, if you have the 2.5 inch exhaust manifold, chances are you will also have to swap the intake as it is not the same as on the old motor.
All that being said, I'm really not sure after you have swapped all the required parts to fit the new motor in the truck that the new ECM will behave appropriately with much less air coming and much more restrictions coming out...
Best way of determining if you have the appropriate motor for your year/application, is to take both motor's valve covers off and comparing the front timing gears. IF they don't have the same number of teeth then the new motor will not fit your application.