The 2.9L and the 4.0L for all intents and purpose are the same block. Ford bored and stroked it to maximize the displacement for that block. The only major change is when they switched it from a pushrod V6 to a SOHC V6.
Is your current 2.9L Carbed or EFI? If it is carbed, switch the intakes and distributor and you are ready to go. If it is EFI, its best to get a newer automatic with wire harness and computer. The 4.0 uses coil packs and sensor instead of traditional Coil and distributor.