I put a 1.25" JKS body lift on my rig, and it did make it a bit harder to get into the rearward gears (2,4,R). I simply moved my console back about 1/4" and remounted it. Cured the problem for $0. The rear section of the console I elongated the holes, the front section I re-drilled the mount. Careful when you pop the rubber boot, the plastic likes to break.
Edit: I did install a 1" Motor Mount lift at the same time as the body lift.