Unlike your 1993, the 2001 4.0 lacks a distributor - using, instead, Coil On Plug (COP) ignition.
You can probably mount a distributor to the engine (I believe it's the same casting as the earlier OBD-II blocks, so it's got to have some sort of fuel pump drive) and retrofit it - I'd probably use your 1993 distributor so I'd not have to worry about anything. CHECK.
Removing the COP ignition will result in some bolt holes on the head that aren't being used, but I'm fairly sure they're blind, and don't NEED to be plugged (although I'd put short bolts in them just for the sake of a "finished" look.)
That's the biggest block I can think of - everything else should just bolt right over. I'd be highly inclined to use the 1993 head on the 2001 block - but again, that's just me (if I were closer, I'd ask you for the head for my own uses. Probably dissection for research, or porting experiments...)
5-90