Usually, the two biggest culprits for limiting down travel are the track bar and the factory steering components.
With most 4" liftkits, you leave the axle mount alone and use some kind of custom made piece that bolts into the stock bracket on the unibody. Other kits just supply a new track bar that's longer and uses a TRE in the upper bracket like the factory one.
The track bar moves down with the suspension, but the suspension wants to drop straight down when both wheels are off the ground. The track bar sort of swings down on an arc and actually pulls the entire axle to the driver's side the farther down it moves. Because of this, you'll notice that the drivers side tire will drop down a little farther than the passenger side.
When the front axle is dropped down as far as it will go, you'll see that the track bar is likely making contact with the lower mount on the axle. Removing the track bar and using a sawzall to trim about 3/4" of the top edge of that bracket will give you just a bit more drop. If you have a track bar that is slightly adjustable (usually at the top, TRE end) you can turn the TRE farther inside the track bar, then put the lower end back into the lower bracket - note how far the bushing is now to the right and drill a new hole there. That will give you just a bit more drop.
Now, your factory steering does basically the same thing as the track bar - it travels down in an arc from the pitman arm to the pass. side knuckle. It will want to pull your steering to the left when nearing full drop.
As far as your upper and lower control arms, well, you'll need to get the jeep on jack stands high enough to allow the axle to drop as far as it can and see where the control arms make contact with where they're mounted. Just like the lower track bar mount, you can trim the ends of the lower control arm mounts on the axle just below the coil spring perch. Upper control arms usually don't bind much, but control arms all drop in an arc as well. The upper control arms are usually maxed out at full drop and not much can be done without buying Rubicon Express' drop bracket kit with adjustable upper arms.
Like someone mentioned before, be sure your brake lines have plenty of slack before going and dropping your suspension - you can usually get a bit more length by removing the bolt that holds the "L" bracket to the unibody in the wheel well, pulling down and out on the solid brake line and then mounting the "L" bracket in it's new, lower position. Usually this can get you 3-4" more length. Usually the lift kit instructions already require you to do this.
The ultimate solution? Invest in the R.E. drop bracket kit, R.E. adjustable control arms, and a heavy duty track bar and track bar bracket. But, doing just a bit of trimming, relocating mounting locations, and dropping the brake lines a bit more will be the cheapest route to a bit more drop.
Ya dig?
Troy