I'm doing similar to my MJ with 1/4". The only section that needed to be done was from where the LCA pockets used to be to where the unibody widens on a MJ (just behind the tranny Xmember), only 21" total. I bought some 4x4x.250 box and cut the top off, then realized that it wont fit over that section. So I bought 4x6x.250 angle and some .250 plate to build my own channel, but with a weird ass taper... I also cut some 1" holes in the bottom of it and welded 1 1/8th nuts to the inside of it, then cut 1 1/4" holes (had to be bored out) in the unibody to recess the nuts in. It gives a really solid place to mount skidplats (future) and my stupid rusty's Xmember. I'm going to reuse the box and plate farther back from there, no sense wasting the steel.
1/4" is way overkill. Like, stupid overkill; especially if you're going to bolt a skidplate underneath it. I'd suggest cutting lots of holes in the sides of the box/channe/angle for rosette (is that how it's spelled?) welds, so you can get more surface area to spread the welds over the thin unibody. I'd weld along the top for 2" every 3" or so too; although I just said f'ck it with mine and laid 21" of weld. For stress dissipation that assumably is a no-no, but I doubt it's going to be an issue. Oh yeah, don't bother with rosettes on the bottom, welding upside-down above your head is just plain not worth the trouble...
Using channel is probably the easier way. I was just afraid it wouldn't fit because of how it was tapered, and didn't feel like buying a peice to find out.