No, it wont. The 2.9 and 3.0 are different patterns. With that said, with money anything can be made to fit. The 2.3 and 2.9 trannys are also built to only handle what those two motors put out; the SHO motor will make short work of them.
Jeff, a SHO buggy guy in Tucson has a friend that put a SHO motor into a Bronco II frame and built a roll cage on top of the frame. It is an automatic and it hauls A$$. He takes it on long desert rides with true buggies and quads, and none of the quad riders want to be ahead of him in the line-up. He puts it in low-range and lets the automatic do its job. I've got pics of it somewhere, I'll try and find them. He did say that an aftermarket tranny cooler is a must.
Tom