There is no such thing as a 4.0L Bronco II. Well, there is, but it's called an Explorer.
2.9L M5OD-R1s do exist, though they are fairly rare in 4x4 form, and they will work fine. The gear ratios are slightly different. 3.0L versions will NOT work, and neither will any 4banger form.
Sources for 4.0Ls are almost all Explorers (excepting the later ones that had 5.0Ls), some Aerostars and some Rangers.