If you put your X on a lift and let the suspension hang down, you're at "full droop" when the suspension is a far as it can travel down from the frame. On the other hand, when something pushes the suspension up as far as it can go toward the frame, that's the extreme of your bump travel, when the suspension is at it's most compressed. Unless something gets in the way, at full compression, especially if there's some hard force at work, the axle may contact the frame in the rear, for example. This is what people usually mean by "bottoming out."
Bumpstops, and there are many kinds, prevent, impede and/or dampen this kind of unwanted contact. Notoriously, our stock bumpstops prove inadequate to this task for people who drive hard off-road or who load the X down with people and gear. There are a number of aftermarket solutions.
It's not really our bumpstops that are inadequate for our rear suspension. It is our leaf spring strength and progression. The Timbren bumpstops in the rear mask the real issue and make it more tolerable. A multi-leaf add-a-leaf pretty much takes care of the real problem and upgraded bumpstops are not needed.
The bottoming out we get is the harsh contact of either the overload leaf against the main springs or the total rear suspension hitting the bumpstops quickly. Unless we stick a camera under there and see the impact it's really hard to speculate and seperate the two. Again the better bumpstops will just mask the impact and make it less harsh, but a better spring pack or AAL is the real cure. A better rear shock with good dampening will also lesson the impact.
The AAL typically gives around 1.5" of lift by themselves, so you would not need the shackle to match the front lift. PRG's Deave mini pack ($149 w/free shipping) works very well, has easy install, will eliminate "bottoming out", and now will come with a shim as I'm told by Greg at PRG.
I'm thinking you will need a longer bumpstop in the front since you are just pushing the coilover downward (Autozone's will work), but with the Deaver's in the rear you won't need any different than stock for the rear.