I didn't actually. The new lift I have says it comes with upgraded bump stops for it. It's an iron rock 3"
33 is still a lot of tire for 3 inch lift on a WJ. I would research how to set bump stops properly especially since you will have it all apart again. It's way easier to do with coils and sway bar links off. The easiest way to describe it is with coils removed, put tires back on and jack up that side of the axle where your tire is close to hitting the fender (where ever you decide you want it to stop), then look at how close your bump stop is to the axle. Keep in mind the bump stop compresses as well, it's not a fully rigid piece of rubber. Then adjust accordingly. Keep in mind you also have to concern yourself with shocks bottoming out.
Basically you want your axle to hit full bump before your tires hit the fenders AND that your shocks don't bottom out as well.
EDIT: Just found this link too:
http://wayalife.com/showthread.php?35447-2-questions-shock-and-bump-stop-length
Also, I was told by two WJers that rock crawl way harder than I do, that the brake lines do not need to be extended if you disconnect your sway bar links. Research this on your own, but the lines run parallel to your LCAs and don't seem to be affected until you get into 6 inch lifts.