Good info! As someone who's been through this recently (several times on my Jeep and a couple of others), while you have the header off and everything out of the way, take a good look at your motor mounts, especially the drivers side. If they are in bad shape, your new manifold will crack eventually. Mine lasted about 6 months and this is why:
Great time to replace them is while you already have everything off. Even if you don't have much money and want to go with OEM replacements from your favorite parts house vs. ordering after market ones online.
No leaks and no modification to the manifold (I still have the old style intake on my 97).
I'd like to upgrade to the later model intake with the larger plenum chamber someday.
I'll update how things piece back together when I get around to it.
Fair warning - that might be years from now.
I did want to mention that I was surprised at the improved throttle response.
The mud terrains will chirp and break loose with much less persuasion from the skinny pedal now.
I reset the throttle cable and the CPU as described on go-jeep, I believe this helped a lot.
The APN header also gave the 4.0 a very pleasing throaty rumble.
Of course, it is much quieter than the stock header with that crack!
Under hood temps have also notably dropped.