Is it safe to assume you have a manual? If so, manuals wouldn't have the same problem as an automatic.
I also see that you also have a 2-door, how many miles have you put on it since your lift? I personally haven't seen a 2-door with 3" or more lift have a rear drive shaft survive more than about a year or so or 30,000 miles before the CV boot finally ruptured. But again, what do I know. Unlike you, I'm just trying to give solid advice and not push a specific product that you chose to buy. And really, more power to you for loving as much as you do.
Do you have a manual transmission? If so, that is the reason why. I am specifically talking about 07-11 JK's with an AUTOMATIC transmission here and actually, any 2012-up regardless of transmission. There is NO way you could not be hitting your front drive shaft boot on the transmission with 4.5" of lift at a flex UNLESS your shocks are too short.