Trans won't fit, and pretty much all of the computer stuff, wiring harness, etc, will have to be changed out.
Those engines aren't related...The 2.9 became the 4.0. The 2.8, 2.9, 4.0 are one engine family. The 3.0 is on it's own. Then there are the 2.x Limas, which are another family. THey all use different bolt patterns, and different computers and wiring (to my knowledge).