Possibly, I know that the 45re and 46re are two totally different animals, the 45re is totally computer controlled while the 46re is not, its about 50/50 so the wiring for that will be incompatible. As far as the engine I am not sure, the 5.9 was a batch injector system that is why they don't idle the nicest, and the 4.7 is sequential injected. If you can make that work it would make the 5.9 run a little nicer, but I don't know if it is possible.
The 5.9 pcm may have a different pin-out so I don't know if it would work with the 4.7 harness, you would have to compare harness diagrams to know for sure. That is why if I would of done it I would of put the 5.9 harness and pcm in it.
That is why I recommend you get a good scanner on it to see if the pcm is getting the signals it needs to make it run right. If it is getting the right signals then it you should be able to make it work. With out it, its possible may never run right, this is going to be a project to make this work.