It depends on the lift kit, I put a rough country X series long arm on my 05 and the stock muffler rubs against the control arm. I heard this nasty rattling, after about 500 miles the freakin muffler edge was damn near rattle rubbing through the control arm itself. Rough country replaced the arm no problem and I too a saw to the muffler and cat, I kept the rear portion of the pipe in only because it was impossible to remove it without cutting it around the axle and rear track bar, plus I still needed some type of exhaust. So I filled in the gap with a length of bendable walker exhaust tubing, clamped it on, reinforced the rear pipe with some strapping and no more problems. And no my state doesn't require inspections so I can care less about the cat / muffler combo. I don't mind the sound, it fits my Jeep's profile anyhow
If you have inspections, look into a circular/tubular exhaust kit, plenty out there, if you have basic welding skills you can install them easily.