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Aside from the engine, torque converter, tranny, transfer case, driveshafts, wiring, new fuel pump, fuel tank, fuel lines, accessories, computer, and motor mounts, it shouldn't be a problem.
There is a guy on FullSizeBronco.com that did that swap. It took him a long time and a lot of patience, but he says it was worth it. Plenty of pictures to document, here's the link:
It's about 13 pages worth of his comments on the progress, plus hundreds of other comments by other people telling him how cool it is so there's a bit to wade through. But if I remember right, there's some great pics and he goes into a lot of detail about what he had to do to make it work. I guess there's even a company http://www.fordcummins.com that makes swap parts for it.