If you're talking about simply dropping in a newer Ford mod motor the answer is no. Now, if money is no object that answer can always be turned into a yes, but you're talking LOTS of work including cutting out the shock towers, all new front suspension and fabricating your engine mounts. Those motors are also fuel injected and use a fuel return system I'm sure, so that means all new fuel system from tank to throttle body! It would be very cool but it seems like a whole lotta work to me.
Moving back to the transmission the same answer applies to some extent. Again, you're talking about fabricating new mounts/crossmember and maybe more cutting.
As far as the rearend goes that will be somewhat easier, if they're the same overall width. If not, it's back to cutting the housing and possibly new axles if they can't respline them. You'll also need to do some fabricating to get the brakes online but that isn't too hard.
I'd stick with a 5.0 (old school type) and whatever transmission you decide on and maybe the 8.8" rearend if it fits. Everything except the rearend will be will be a bolt-in with stock Ford parts.
John