Unless your are trying to change the sound of your Jeep or gain marginal performance, my vote is to stick with stock. Don't get me wrong, I love the sound of my Borla system but after my last trip out it is now a very low flow system (hooked it on a rock) that is currently sitting on my garage floor all mangled.
Additionally, do some research to determine if an aftermarket system is truly designed for your year range. Borla claims there system works on all years but it is designed for 97+ with the plastic fuel tank and heat shield so it has a dogleg in it to clear. The problem I had is that on my 91 with ~3" and MJ shackles, the dogleg crashed into the exhaust. Fortunately at the time I had a friend who was good at TIGing SS so we just removed the dogleg.
My $.02