Yes, you remove the bumpstop and leave it out. That means that you must leave no less than 5psi in the bags at all times. This allows the bag to act as a bumpstop and it keeps the bag from becoming pinched between the coils as you flex the suspension. If you ever offroad where you will be flexing a lot, you may need to add some air to the bags to keep the tires from rubbing the fender flares but since you have the stock tires(I assume) you may not need too. I usually use around 15psi offroad.
No, I did not drill a hole in the bottom spring perch for the tube to go through. You can if you like but make 100% sure that the hole it nice and smooth or it will wear a hole in the air line. On my 2004 KJ, it already has a hole in the top of the spring perch, here are all the pics I have from my install, they should answer any questions you have.. Hope that helps.. Dont forget about the MAX air pressure(dont go over it), I believe its around 35psi. They will really stiffen the rear end up making towing much nicer. Make sure you put the air nozzle on the right end before you stick it in the spring! Stupid me had to take it back out of the spring and flip it over..
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I put my air nozzle in an exsisting hole right under the license plate:
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Make sure you DO NOT cut the air line too short. If you run the air line like I did, leave extra air line in the frame rail so as the axle moves up and down the air line will not get pulled off. The air bag will not move up and down within the spring once its pumped up so the air line needs to move with the axle.