Level of difficulty and time frame is not really different than installing a 2.9 clutch. You will need to rewire the 4.0 starter to work with a 4.0 flywheel. Cost of parts depends on where you buy, and whether or not you use a new starter and flywheel, or purchase new. (I wouldn't even consider a used cover/disc) While you're in there I recommend replacing the slave cylinder. You can either trim the blockplate to acomodate the slightly larger snout of the 4.0 starter, or get a manual 4.0 blockplate.
There's lots of info in the tech library, do a search for a complete list of parts.
Advantages? A lot better clamping force due to a 10 inch disc, as opposed to the 8 1/2 2.9 disc. Having done many of these swaps on my own trucks (as well as customers) it's definately worth it.
Good luck!