Well, I'll weigh in on this.
MAF mod on the 4.0 is much higher risk than on the 3.0 (where ther is virtually NO risk except the warranty issues Dave and Julie brought up). My 3.0 has been modded for almost 2 years and it runs fine (it's a 2002).
2004 MAF's are quite different. They have the MAF mod already built in, basically. The sensor is a different design entirely and results in much less blocking of the intake. I like it.
Yes, the IAT is in the MAF, but the MAF mod won't affect it. I would say about 1 in 4 of the 4.0 MAF mods I've done has had a problem, and about 1/2 of them were too much to live with.
There were some rare cases of MAF swaps by dealers after modding; but they were special cases where the dealer had an extra for some reason and they knew the truck owner well. Not something you should count on. Taking a hacksaw to your MAF is NOT covered under the warranty except by the grace of the service department!
So although I have done MAF mod's on 4.0's, I always advise against it. Many people want to do it anyway so I do it for them -- but no one can guarantee what the result will be. 4.0's are much more finicky about idle air metering than the 3.0 engines are.