Cooling isn't an issue, but electronics can be.
However, since the lower half of the engine is essentially the same, why not rebuild the lower half, put on a newer head, and come out farther ahead than you were when you started? Apart from the electronics (deletion of the knock sensor, changed the HEGO sensor, HO Tbody/TPS different, and a few other things I just don't feel like looking up right now...) the principal difference between the two engines is the cylinder head. The blocks are mechanically the same all the way from 1987-2001, with the only differences really being the knock sensor boss going unmachined (starting in 1991) and the addition of the main stud girdle (beginning in 1994 - but can be added to any 4.0 if you get the right main bolts.)
The cylinder heads were changed a couple times, with casting #7120 being accepted as the best.
Also, you could rebuild your bottom end, and try a copy of the new aftermarket head that's out now - you can get them from quite a few people (but HESCO started it...) The newer head is supposed to breathe even better than the 7120, accepts roller or stamped rockers, and the aluminum allows/requires you to run high compression - which can translate to more torque. I also like the fact that they made the lifter bores bigger - you can pull lifters without pulling the head! (that was a big point when we were discussing a "clean sheet" cylinder head in, say, 1Q2001 or so...)
Mechanically, there isn't much difference between RENIX/OBD-I/OBD-II engines - the dimensions are the same (inside and out) and the cranks, pistons, and heads interchange. The HO intake and exhaust won't bolt onto the RENIX head - so you just swap the whole thing all at once, and call it done. The exhaust pipe comes up in the same place (probably same flange, to boot) and you get the better-flowing OBD intake manifold and throttle body.
It woud take a little work, but you don't have to swap as much in the way of electronics...
5-90