First off, the 258 is an I6, not a V6. And it's a 4.2, not a 2.8.
Now that that's out of the way, in addition to the complete engine assembly, you'll need:
New engine mount frame brackets
Different bellhousing and/or transmission (if it's an SR4, just throw it out now and be done with it. It's not even a good door stop)
Probably a different wiring harness
Different clutch linkage if it's a manual tranny - the throw on a 4-banger clutch slave isn't quite enough for a 6 from what I've been told
Probably more, but those things spring to mind...
Basically, everything under the hood will need to be replaced except the transfer case.
The good thing is that the axles will already have 3.73 or 4.1 gears in them so you don't have a regearing expense if you want to run 33" tires.