Ranger trans swap question

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I have my 1987 Ranger (still mostly stock for now ), but the transmission is starting to go out. Since i have big plans for this truck I figured that it might be best to start the parts swaps now so I can keep driving it instead of spending the money twice. Anyway, on to the question:

I currently have an FM145 4x4 behind a 2.9L V6. I know most of the differences between the 145 and M5OD, but my big question is, if I replace the mitsu with the newer Mazda trans, what if any shifter hole clearance issues am I going to run into?

I know that the transfer case and shafts are going to need to be changed out too, but for now I am more worried about whether or not I'm gonna put this thing up in there and find that i either can't put the shifter in b/c the attaching point is now under the floor, rather than the hole, or that I can put the shifter in but not be able to use a set of gears (1,3,5/2,4,R)