First, I'll preface my comments by saying anything can be done with enough money and expertise.
Second, the fuel injection systems are entirely different and thus use different sensor. To further compound the situation and add to the complexity, the 3.9L has a cam driven distributor whereas the 4.0L uses coil packs. While the majority of these issues can be overcome with swapping the front engine cover, installing a different cam, ect, ect.
There is one issue that has always scared me and that is cutting the block and routing the wiring for the crank sensor. There is very little room for error. Oh, and while thinking about that, the flex plate in the 3.9L is different and doesn't have the serrated plate for the crank sensor to read.
Let's see, you'll also need to drill holes in the block for NOX sensors. So in the end, you'll need to do surgery on the block for the NOX sensors and the crank senspr. The first is easy. Ask around about the second because I know of no one who has done the work. Finally, you will also be undoing a number of things that should have been recently done on the rebuild of the 3.9L like changing the cam, removing the engine cover complete with it's freshly redone oil pump and ditching the plenum with it's sensors.
I don't know if I would try this sort of undertaking. It's a lot easier to go from a 4.)L back to a 3.(L (I've done that). There should be enough 4.0L's out there that you can find a replacement to fit your budget.
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