If it even bolts to the engine (remember a new engine as well) you now need a computer to shift it. The new engine is a different size, different HP, surely different power curves. How will you get a computer for a 5-speed to work on a 9-speed? Or more correctly how will you get a computer that is expected to talk to a new engine talk to the old engine?
I'm just going to say, no. There will not be any putting the 9-speed behind the 4.0 engine.
Someone (in many years) might take a '20 and gut it and put it into an old body shell. Which will be a bit pointless since the '20 is the same old truck just a new engine and transmission. So even that isn't likely, except to maybe rebuild a couple wrecked trucks into one.