I can understand the idea of increasing airflow, but what else are you doing to offset this mod?
The basic airflow properties of the 4.0 head are not bad to begin with, and the limiting factor for you will end up being the throttle body. To take full advantage of the "big valve" head (I'm assuming you're trying 2.02/1.60 valves like Mike Parrish at Accurate Power uses) without using a blower or a turbo, you are going to need to replace the throttle body, or just have it bored out to begin with.
Also, if any work has been done to expand the port size of the head in conjunction with the valve work, you are going to move your power band up thru the RPM range and lose low-end power - which is the hallmark of the inline six engine! If you haven't increased port size, flow increases are still useful, but may not give you the results you are hoping for...
All else being equal, while I like the look of going to 2.02/1.60 valves for the head (and the concomitant increase in parts options,) I'd probably not go bigger on the valves without planning on forced induction as another mod.
I am sure I will hear from someone else saying that the "big valve" setup is not a bad thing, and I am always willing to be convinced, but that's my story and I'm stickin' to it!
All that being said, was the 2.02/1.60 setup an end in itself for you, or do you plan on doing anything else? At the very least, I'd toss on an aftermarket equal-length header, open up the rest of the exhaust, and bore out the throttle body. If you have the HO head, it would also be worth thinking of finding a 1999-2001 intake manifold, as it flows better and has been "tuned" to the power band of the 4.0 mill, saving you the need to build one of your own...
Lastly, it's your Jeep and you should enjoy it. However, there's nothing wrong with having your beliefs challenged - it will probably result in new ideas and a better end result...
5-90